diff --git a/Source/Core/Common/Config/Layer.cpp b/Source/Core/Common/Config/Layer.cpp
@@ -8,10 +8,47 @@
 
 #include "Common/Config/Config.h"
 #include "Common/Config/Layer.h"
-#include "Common/Config/Section.h"
 
 namespace Config
 {
+namespace detail
+{
+std::string ValueToString(u16 value)
+{
+  return StringFromFormat("0x%04x", value);
+}
+
+std::string ValueToString(u32 value)
+{
+  return StringFromFormat("0x%08x", value);
+}
+
+std::string ValueToString(float value)
+{
+  return StringFromFormat("%#.9g", value);
+}
+
+std::string ValueToString(double value)
+{
+  return StringFromFormat("%#.17g", value);
+}
+
+std::string ValueToString(int value)
+{
+  return std::to_string(value);
+}
+
+std::string ValueToString(bool value)
+{
+  return StringFromBool(value);
+}
+
+std::string ValueToString(const std::string& value)
+{
+  return value;
+}
+}
+
 ConfigLayerLoader::ConfigLayerLoader(LayerType layer) : m_layer(layer)
 {
 }
@@ -38,64 +75,56 @@ Layer::~Layer()
   Save();
 }
 
-bool Layer::Exists(System system, const std::string& section_name, const std::string& key)
+bool Layer::Exists(const ConfigLocation& location) const
 {
-  Section* section = GetSection(system, section_name);
-  if (!section)
-    return false;
-  return section->Exists(key);
+  const auto iter = m_map.find(location);
+  return iter != m_map.end() && iter->second.has_value();
 }
 
-bool Layer::DeleteKey(System system, const std::string& section_name, const std::string& key)
+bool Layer::DeleteKey(const ConfigLocation& location)
 {
-  Section* section = GetSection(system, section_name);
-  if (!section)
-    return false;
-  return section->Delete(key);
+  m_is_dirty = true;
+  bool had_value = m_map[location].has_value();
+  m_map[location].reset();
+  return had_value;
 }
 
-Section* Layer::GetSection(System system, const std::string& section_name)
+void Layer::DeleteAllKeys()
 {
-  for (auto& section : m_sections[system])
-    if (!strcasecmp(section->m_name.c_str(), section_name.c_str()))
-      return section.get();
-  return nullptr;
+  m_is_dirty = true;
+  for (auto& pair : m_map)
+  {
+    pair.second.reset();
+  }
 }
 
-Section* Layer::GetOrCreateSection(System system, const std::string& section_name)
+Section Layer::GetSection(System system, const std::string& section)
 {
-  Section* section = GetSection(system, section_name);
-  if (!section)
-  {
-    if (m_layer == LayerType::Meta)
-    {
-      m_sections[system].emplace_back(
-          std::make_unique<RecursiveSection>(m_layer, system, section_name));
-    }
-    else
-    {
-      m_sections[system].emplace_back(std::make_unique<Section>(m_layer, system, section_name));
-    }
-    section = m_sections[system].back().get();
-  }
-  return section;
+  return Section{m_map.lower_bound(ConfigLocation{system, section, ""}),
+                 m_map.lower_bound(ConfigLocation{system, section + '\001', ""})};
+}
+
+ConstSection Layer::GetSection(System system, const std::string& section) const
+{
+  return ConstSection{m_map.lower_bound(ConfigLocation{system, section, ""}),
+                      m_map.lower_bound(ConfigLocation{system, section + '\001', ""})};
 }
 
 void Layer::Load()
 {
   if (m_loader)
     m_loader->Load(this);
-  ClearDirty();
+  m_is_dirty = false;
   InvokeConfigChangedCallbacks();
 }
 
 void Layer::Save()
 {
-  if (!m_loader || !IsDirty())
+  if (!m_loader || !m_is_dirty)
     return;
 
   m_loader->Save(this);
-  ClearDirty();
+  m_is_dirty = false;
   InvokeConfigChangedCallbacks();
 }
 
@@ -106,44 +135,6 @@ LayerType Layer::GetLayer() const
 
 const LayerMap& Layer::GetLayerMap() const
 {
-  return m_sections;
-}
-
-bool Layer::IsDirty() const
-{
-  return std::any_of(m_sections.begin(), m_sections.end(), [](const auto& system) {
-    return std::any_of(system.second.begin(), system.second.end(),
-                       [](const auto& section) { return section->IsDirty(); });
-  });
-}
-
-void Layer::ClearDirty()
-{
-  std::for_each(m_sections.begin(), m_sections.end(), [](auto& system) {
-    std::for_each(system.second.begin(), system.second.end(),
-                  [](auto& section) { section->ClearDirty(); });
-  });
-}
-
-RecursiveLayer::RecursiveLayer() : Layer(LayerType::Meta)
-{
-}
-
-Section* RecursiveLayer::GetSection(System system, const std::string& section_name)
-{
-  // Always queries backwards recursively, so it doesn't matter if it exists or not on this layer
-  return GetOrCreateSection(system, section_name);
-}
-
-Section* RecursiveLayer::GetOrCreateSection(System system, const std::string& section_name)
-{
-  Section* section = Layer::GetSection(system, section_name);
-  if (!section)
-  {
-    m_sections[system].emplace_back(
-        std::make_unique<RecursiveSection>(m_layer, system, section_name));
-    section = m_sections[system].back().get();
-  }
-  return section;
+  return m_map;
 }
 }
diff --git a/Source/Core/Common/Config/Layer.h b/Source/Core/Common/Config/Layer.h
@@ -6,18 +6,47 @@
 
 #include <map>
 #include <memory>
+#include <optional>
 #include <string>
 #include <vector>
 
+#include "Common/Config/ConfigInfo.h"
 #include "Common/Config/Enums.h"
-#include "Common/Config/Section.h"
+#include "Common/StringUtil.h"
 
 namespace Config
 {
+namespace detail
+{
+std::string ValueToString(u16 value);
+std::string ValueToString(u32 value);
+std::string ValueToString(float value);
+std::string ValueToString(double value);
+std::string ValueToString(int value);
+std::string ValueToString(bool value);
+std::string ValueToString(const std::string& value);
+
+template <typename T>
+std::optional<T> TryParse(const std::string& str_value)
+{
+  T value;
+  if (!::TryParse(str_value, &value))
+    return std::nullopt;
+  return value;
+}
+
+template <>
+inline std::optional<std::string> TryParse(const std::string& str_value)
+{
+  return str_value;
+}
+}
+
 template <typename T>
 struct ConfigInfo;
 
-using LayerMap = std::map<System, std::vector<std::unique_ptr<Section>>>;
+class Layer;
+using LayerMap = std::map<ConfigLocation, std::optional<std::string>>;
 
 class ConfigLayerLoader
 {
@@ -33,6 +62,30 @@ class ConfigLayerLoader
   const LayerType m_layer;
 };
 
+class Section
+{
+public:
+  using iterator = LayerMap::iterator;
+  Section(iterator begin_, iterator end_) : m_begin(begin_), m_end(end_) {}
+  iterator begin() const { return m_begin; }
+  iterator end() const { return m_end; }
+private:
+  iterator m_begin;
+  iterator m_end;
+};
+
+class ConstSection
+{
+public:
+  using iterator = LayerMap::const_iterator;
+  ConstSection(iterator begin_, iterator end_) : m_begin(begin_), m_end(end_) {}
+  iterator begin() const { return m_begin; }
+  iterator end() const { return m_end; }
+private:
+  iterator m_begin;
+  iterator m_end;
+};
+
 class Layer
 {
 public:
@@ -41,34 +94,45 @@ class Layer
   virtual ~Layer();
 
   // Convenience functions
-  bool Exists(System system, const std::string& section_name, const std::string& key);
-  bool DeleteKey(System system, const std::string& section_name, const std::string& key);
+  bool Exists(const ConfigLocation& location) const;
+  bool DeleteKey(const ConfigLocation& location);
+  void DeleteAllKeys();
+
   template <typename T>
-  bool GetIfExists(System system, const std::string& section_name, const std::string& key, T* value)
+  T Get(const ConfigInfo<T>& config_info)
   {
-    if (Exists(system, section_name, key))
-      return GetOrCreateSection(system, section_name)->Get(key, value);
-
-    return false;
+    return Get<T>(config_info.location).value_or(config_info.default_value);
   }
 
-  virtual Section* GetSection(System system, const std::string& section_name);
-  virtual Section* GetOrCreateSection(System system, const std::string& section_name);
-
   template <typename T>
-  T Get(const ConfigInfo<T>& config_info)
+  std::optional<T> Get(const ConfigLocation& location)
   {
-    return GetOrCreateSection(config_info.location.system, config_info.location.section)
-        ->template Get<T>(config_info.location.key, config_info.default_value);
+    const std::optional<std::string>& str_value = m_map[location];
+    if (!str_value)
+      return std::nullopt;
+    return detail::TryParse<T>(*str_value);
   }
 
   template <typename T>
   void Set(const ConfigInfo<T>& config_info, const T& value)
   {
-    GetOrCreateSection(config_info.location.system, config_info.location.section)
-        ->Set(config_info.location.key, value);
+    Set<T>(config_info.location, value);
   }
 
+  template <typename T>
+  void Set(const ConfigLocation& location, const T& value)
+  {
+    const std::string new_value = detail::ValueToString(value);
+    std::optional<std::string>& current_value = m_map[location];
+    if (current_value == new_value)
+      return;
+    m_is_dirty = true;
+    current_value = new_value;
+  }
+
+  Section GetSection(System system, const std::string& section);
+  ConstSection GetSection(System system, const std::string& section) const;
+
   // Explicit load and save of layers
   void Load();
   void Save();
@@ -77,19 +141,9 @@ class Layer
   const LayerMap& GetLayerMap() const;
 
 protected:
-  bool IsDirty() const;
-  void ClearDirty();
-
-  LayerMap m_sections;
+  bool m_is_dirty = false;
+  LayerMap m_map;
   const LayerType m_layer;
   std::unique_ptr<ConfigLayerLoader> m_loader;
 };
-
-class RecursiveLayer final : public Layer
-{
-public:
-  RecursiveLayer();
-  Section* GetSection(System system, const std::string& section_name) override;
-  Section* GetOrCreateSection(System system, const std::string& section_name) override;
-};
 }
diff --git a/Source/Core/Common/Config/Section.cpp b/Source/Core/Common/Config/Section.cpp
diff --git a/Source/Core/Common/Config/Section.h b/Source/Core/Common/Config/Section.h
diff --git a/Source/Core/Core/BootManager.cpp b/Source/Core/Core/BootManager.cpp
@@ -376,7 +376,7 @@ bool BootCore(std::unique_ptr<BootParameters> boot)
 
   // Ensure any new settings are written to the SYSCONF
   if (StartUp.bWii)
-    ConfigLoaders::SaveToSYSCONF(Config::GetLayer(Config::LayerType::Meta));
+    ConfigLoaders::SaveToSYSCONF(Config::LayerType::Meta);
 
   const bool load_ipl = !StartUp.bWii && !StartUp.bHLE_BS2 &&
                         std::holds_alternative<BootParameters::Disc>(boot->parameters);

diff --git a/Source/Core/Core/Config/MainSettings.cpp b/Source/Core/Core/Config/MainSettings.cpp
@@ -61,6 +61,7 @@ ConfigInfo<bool> GetInfoForSimulateKonga(u32 channel)
 }
 
 const ConfigInfo<bool> MAIN_WII_SD_CARD{{System::Main, "Core", "WiiSDCard"}, false};
+const ConfigInfo<bool> MAIN_WII_SD_CARD_WRITABLE{{System::Main, "Core", "WiiSDCardWritable"}, true};
 const ConfigInfo<bool> MAIN_WII_KEYBOARD{{System::Main, "Core", "WiiKeyboard"}, false};
 const ConfigInfo<bool> MAIN_WIIMOTE_CONTINUOUS_SCANNING{
     {System::Main, "Core", "WiimoteContinuousScanning"}, false};

diff --git a/Source/Core/Core/Config/MainSettings.h b/Source/Core/Core/Config/MainSettings.h
@@ -40,6 +40,7 @@ ConfigInfo<u32> GetInfoForSIDevice(u32 channel);
 ConfigInfo<bool> GetInfoForAdapterRumble(u32 channel);
 ConfigInfo<bool> GetInfoForSimulateKonga(u32 channel);
 extern const ConfigInfo<bool> MAIN_WII_SD_CARD;
+extern const ConfigInfo<bool> MAIN_WII_SD_CARD_WRITABLE;
 extern const ConfigInfo<bool> MAIN_WII_KEYBOARD;
 extern const ConfigInfo<bool> MAIN_WIIMOTE_CONTINUOUS_SCANNING;
 extern const ConfigInfo<bool> MAIN_WIIMOTE_ENABLE_SPEAKER;

diff --git a/Source/Core/Core/ConfigLoaders/BaseConfigLoader.cpp b/Source/Core/Core/ConfigLoaders/BaseConfigLoader.cpp
@@ -26,7 +26,7 @@
 
 namespace ConfigLoaders
 {
-void SaveToSYSCONF(Config::Layer* layer)
+void SaveToSYSCONF(Config::LayerType layer)
 {
   if (Core::IsRunning())
     return;
@@ -40,9 +40,9 @@ void SaveToSYSCONF(Config::Layer* layer)
           const std::string key = info.location.section + "." + info.location.key;
 
           if (setting.type == SysConf::Entry::Type::Long)
-            sysconf.SetData<u32>(key, setting.type, layer->Get(info));
+            sysconf.SetData<u32>(key, setting.type, Config::Get(layer, info));
           else if (setting.type == SysConf::Entry::Type::Byte)
-            sysconf.SetData<u8>(key, setting.type, static_cast<u8>(layer->Get(info)));
+            sysconf.SetData<u8>(key, setting.type, static_cast<u8>(Config::Get(layer, info)));
         },
         setting.config_info);
   }
@@ -77,9 +77,9 @@ class BaseConfigLayerLoader final : public Config::ConfigLayerLoader
 {
 public:
   BaseConfigLayerLoader() : ConfigLayerLoader(Config::LayerType::Base) {}
-  void Load(Config::Layer* config_layer) override
+  void Load(Config::Layer* layer) override
   {
-    LoadFromSYSCONF(config_layer);
+    LoadFromSYSCONF(layer);
     for (const auto& system : system_to_ini)
     {
       IniFile ini;
@@ -89,55 +89,62 @@ class BaseConfigLayerLoader final : public Config::ConfigLayerLoader
       for (const auto& section : system_sections)
       {
         const std::string section_name = section.GetName();
-        Config::Section* config_section =
-            config_layer->GetOrCreateSection(system.first, section_name);
         const IniFile::Section::SectionMap& section_map = section.GetValues();
 
         for (const auto& value : section_map)
-          config_section->Set(value.first, value.second);
+        {
+          const Config::ConfigLocation location{system.first, section_name, value.first};
+          layer->Set(location, value.second);
+        }
       }
     }
   }
 
-  void Save(Config::Layer* config_layer) override
+  void Save(Config::Layer* layer) override
   {
-    const Config::LayerMap& sections = config_layer->GetLayerMap();
-    for (const auto& system : sections)
+    SaveToSYSCONF(layer->GetLayer());
+
+    std::map<Config::System, IniFile> inis;
+
+    for (const auto& system : system_to_ini)
     {
-      if (system.first == Config::System::SYSCONF)
-      {
-        SaveToSYSCONF(config_layer);
+      inis[system.first].Load(File::GetUserPath(system.second));
+    }
+
+    for (const auto& config : layer->GetLayerMap())
+    {
+      const Config::ConfigLocation& location = config.first;
+      const std::optional<std::string>& value = config.second;
+
+      // Done by SaveToSYSCONF
+      if (location.system == Config::System::SYSCONF)
         continue;
-      }
 
-      auto mapping = system_to_ini.find(system.first);
-      if (mapping == system_to_ini.end())
+      auto ini = inis.find(location.system);
+      if (ini == inis.end())
       {
         ERROR_LOG(COMMON, "Config can't map system '%s' to an INI file!",
-                  Config::GetSystemName(system.first).c_str());
+                  Config::GetSystemName(location.system).c_str());
         continue;
       }
 
-      IniFile ini;
-      ini.Load(File::GetUserPath(mapping->second));
+      if (!IsSettingSaveable(location))
+        continue;
 
-      for (const auto& section : system.second)
+      if (value)
       {
-        const std::string section_name = section->GetName();
-        const Config::SectionValueMap& section_values = section->GetValues();
-
-        IniFile::Section* ini_section = ini.GetOrCreateSection(section_name);
-
-        for (const auto& value : section_values)
-        {
-          if (!IsSettingSaveable({system.first, section->GetName(), value.first}))
-            continue;
-
-          ini_section->Set(value.first, value.second);
-        }
+        IniFile::Section* ini_section = ini->second.GetOrCreateSection(location.section);
+        ini_section->Set(location.key, *value);
       }
+      else
+      {
+        ini->second.DeleteKey(location.section, location.key);
+      }
+    }
 
-      ini.Save(File::GetUserPath(mapping->second));
+    for (const auto& system : system_to_ini)
+    {
+      inis[system.first].Save(File::GetUserPath(system.second));
     }
   }
 
@@ -153,13 +160,10 @@ class BaseConfigLayerLoader final : public Config::ConfigLayerLoader
       std::visit(
           [&](auto& info) {
             const std::string key = info.location.section + "." + info.location.key;
-            auto* section =
-                layer->GetOrCreateSection(Config::System::SYSCONF, info.location.section);
-
             if (setting.type == SysConf::Entry::Type::Long)
-              section->Set(info.location.key, sysconf.GetData<u32>(key, info.default_value));
+              layer->Set(info.location, sysconf.GetData<u32>(key, info.default_value));
             else if (setting.type == SysConf::Entry::Type::Byte)
-              section->Set(info.location.key, sysconf.GetData<u8>(key, info.default_value));
+              layer->Set(info.location, sysconf.GetData<u8>(key, info.default_value));
           },
           setting.config_info);
     }

diff --git a/Source/Core/Core/ConfigLoaders/BaseConfigLoader.h b/Source/Core/Core/ConfigLoaders/BaseConfigLoader.h
@@ -9,11 +9,11 @@
 namespace Config
 {
 class ConfigLayerLoader;
-class Layer;
+enum class LayerType;
 }
 
 namespace ConfigLoaders
 {
-void SaveToSYSCONF(Config::Layer* layer);
+void SaveToSYSCONF(Config::LayerType layer);
 std::unique_ptr<Config::ConfigLayerLoader> GenerateBaseConfigLoader();
 }
diff --git a/Source/Core/Core/ConfigLoaders/GameConfigLoader.cpp b/Source/Core/Core/ConfigLoaders/GameConfigLoader.cpp
@@ -199,10 +199,10 @@ class INIGameConfigLayerLoader final : public Config::ConfigLayerLoader
   {
   }
 
-  void Load(Config::Layer* config_layer) override
+  void Load(Config::Layer* layer) override
   {
     IniFile ini;
-    if (config_layer->GetLayer() == Config::LayerType::GlobalGame)
+    if (layer->GetLayer() == Config::LayerType::GlobalGame)
     {
       for (const std::string& filename : GetGameIniFilenames(m_id, m_revision))
         ini.Load(File::GetSysDirectory() + GAMESETTINGS_DIR DIR_SEP + filename, true);
@@ -217,16 +217,16 @@ class INIGameConfigLayerLoader final : public Config::ConfigLayerLoader
 
     for (const auto& section : system_sections)
     {
-      LoadFromSystemSection(config_layer, section);
+      LoadFromSystemSection(layer, section);
     }
 
-    LoadControllerConfig(config_layer);
+    LoadControllerConfig(layer);
   }
 
-  void Save(Config::Layer* config_layer) override;
+  void Save(Config::Layer* layer) override;
 
 private:
-  void LoadControllerConfig(Config::Layer* config_layer) const
+  void LoadControllerConfig(Config::Layer* layer) const
   {
     // Game INIs can have controller profiles embedded in to them
     static const std::array<char, 4> nums = {{'1', '2', '3', '4'}};
@@ -244,115 +244,89 @@ class INIGameConfigLayerLoader final : public Config::ConfigLayerLoader
       std::string type = std::get<0>(use_data);
       std::string path = "Profiles/" + std::get<1>(use_data) + "/";
 
-      Config::Section* control_section =
-          config_layer->GetOrCreateSection(std::get<2>(use_data), "Controls");
+      const auto control_section = [&](std::string key) {
+        return Config::ConfigLocation{std::get<2>(use_data), "Controls", key};
+      };
 
       for (const char num : nums)
       {
-        bool use_profile = false;
-        std::string profile;
-        if (control_section->Exists(type + "Profile" + num))
+        if (auto profile = layer->Get<std::string>(control_section(type + "Profile" + num)))
         {
-          if (control_section->Get(type + "Profile" + num, &profile))
+          std::string ini_path = File::GetUserPath(D_CONFIG_IDX) + path + *profile + ".ini";
+          if (!File::Exists(ini_path))
           {
-            if (File::Exists(File::GetUserPath(D_CONFIG_IDX) + path + profile + ".ini"))
-            {
-              use_profile = true;
-            }
-            else
-            {
-              // TODO: PanicAlert shouldn't be used for this.
-              PanicAlertT("Selected controller profile does not exist");
-            }
+            // TODO: PanicAlert shouldn't be used for this.
+            PanicAlertT("Selected controller profile does not exist");
+            continue;
           }
-        }
 
-        if (use_profile)
-        {
           IniFile profile_ini;
-          profile_ini.Load(File::GetUserPath(D_CONFIG_IDX) + path + profile + ".ini");
+          profile_ini.Load(ini_path);
 
           const IniFile::Section* ini_section = profile_ini.GetOrCreateSection("Profile");
           const IniFile::Section::SectionMap& section_map = ini_section->GetValues();
           for (const auto& value : section_map)
           {
-            Config::Section* section = config_layer->GetOrCreateSection(
-                std::get<2>(use_data), std::get<1>(use_data) + num);
-            section->Set(value.first, value.second);
+            Config::ConfigLocation location{std::get<2>(use_data), std::get<1>(use_data) + num,
+                                            value.first};
+            layer->Set(location, value.second);
           }
         }
       }
     }
   }
 
-  void LoadFromSystemSection(Config::Layer* config_layer, const IniFile::Section& section) const
+  void LoadFromSystemSection(Config::Layer* layer, const IniFile::Section& section) const
   {
     const std::string section_name = section.GetName();
-    if (section.HasLines())
-    {
-      // Trash INI File chunks
-      std::vector<std::string> chunk;
-      section.GetLines(&chunk, true);
-
-      if (chunk.size())
-      {
-        const auto mapped_config = MapINIToRealLocation(section_name, "");
-
-        if (mapped_config.section.empty() && mapped_config.key.empty())
-          return;
-
-        auto* config_section =
-            config_layer->GetOrCreateSection(mapped_config.system, mapped_config.section);
-        config_section->SetLines(chunk);
-      }
-    }
 
     // Regular key,value pairs
     const IniFile::Section::SectionMap& section_map = section.GetValues();
 
     for (const auto& value : section_map)
     {
-      const auto mapped_config = MapINIToRealLocation(section_name, value.first);
+      const auto location = MapINIToRealLocation(section_name, value.first);
 
-      if (mapped_config.section.empty() && mapped_config.key.empty())
+      if (location.section.empty() && location.key.empty())
         continue;
 
-      auto* config_section =
-          config_layer->GetOrCreateSection(mapped_config.system, mapped_config.section);
-      config_section->Set(mapped_config.key, value.second);
+      layer->Set(location, value.second);
     }
   }
 
   const std::string m_id;
   const u16 m_revision;
 };
 
-void INIGameConfigLayerLoader::Save(Config::Layer* config_layer)
+void INIGameConfigLayerLoader::Save(Config::Layer* layer)
 {
-  if (config_layer->GetLayer() != Config::LayerType::LocalGame)
+  if (layer->GetLayer() != Config::LayerType::LocalGame)
     return;
 
   IniFile ini;
   for (const std::string& file_name : GetGameIniFilenames(m_id, m_revision))
     ini.Load(File::GetUserPath(D_GAMESETTINGS_IDX) + file_name, true);
 
-  for (const auto& system : config_layer->GetLayerMap())
+  for (const auto& config : layer->GetLayerMap())
   {
-    for (const auto& section : system.second)
-    {
-      for (const auto& value : section->GetValues())
-      {
-        if (!IsSettingSaveable({system.first, section->GetName(), value.first}))
-          continue;
+    const Config::ConfigLocation& location = config.first;
+    const std::optional<std::string>& value = config.second;
 
-        const auto ini_location =
-            GetINILocationFromConfig({system.first, section->GetName(), value.first});
-        if (ini_location.first.empty() && ini_location.second.empty())
-          continue;
+    if (!IsSettingSaveable(location))
+      continue;
 
-        IniFile::Section* ini_section = ini.GetOrCreateSection(ini_location.first);
-        ini_section->Set(ini_location.second, value.second);
-      }
+    const auto ini_location = GetINILocationFromConfig(location);
+    if (ini_location.first.empty() && ini_location.second.empty())
+      continue;
+
+    if (value)
+    {
+      IniFile::Section* ini_section = ini.GetOrCreateSection(ini_location.first);
+      ini_section->Set(ini_location.second, *value);
+    }
+    else
+    {
+      ini.DeleteKey(ini_location.first, ini_location.second);
     }
   }
 

diff --git a/Source/Core/Core/ConfigLoaders/MovieConfigLoader.cpp b/Source/Core/Core/ConfigLoaders/MovieConfigLoader.cpp
@@ -46,27 +46,27 @@ static void LoadFromDTM(Config::Layer* config_layer, Movie::DTMHeader* dtm)
   config_layer->Set(Config::GFX_HACK_EFB_EMULATE_FORMAT_CHANGES, dtm->bEFBEmulateFormatChanges);
 }
 
-void SaveToDTM(Config::Layer* config_layer, Movie::DTMHeader* dtm)
+void SaveToDTM(Movie::DTMHeader* dtm)
 {
-  dtm->bDualCore = config_layer->Get(Config::MAIN_CPU_THREAD);
-  dtm->bDSPHLE = config_layer->Get(Config::MAIN_DSP_HLE);
-  dtm->bFastDiscSpeed = config_layer->Get(Config::MAIN_FAST_DISC_SPEED);
-  dtm->CPUCore = config_layer->Get(Config::MAIN_CPU_CORE);
-  dtm->bSyncGPU = config_layer->Get(Config::MAIN_SYNC_GPU);
-  const std::string video_backend = config_layer->Get(Config::MAIN_GFX_BACKEND);
+  dtm->bDualCore = Config::Get(Config::MAIN_CPU_THREAD);
+  dtm->bDSPHLE = Config::Get(Config::MAIN_DSP_HLE);
+  dtm->bFastDiscSpeed = Config::Get(Config::MAIN_FAST_DISC_SPEED);
+  dtm->CPUCore = Config::Get(Config::MAIN_CPU_CORE);
+  dtm->bSyncGPU = Config::Get(Config::MAIN_SYNC_GPU);
+  const std::string video_backend = Config::Get(Config::MAIN_GFX_BACKEND);
 
-  dtm->bProgressive = config_layer->Get(Config::SYSCONF_PROGRESSIVE_SCAN);
-  dtm->bPAL60 = config_layer->Get(Config::SYSCONF_PAL60);
+  dtm->bProgressive = Config::Get(Config::SYSCONF_PROGRESSIVE_SCAN);
+  dtm->bPAL60 = Config::Get(Config::SYSCONF_PAL60);
   if (dtm->bWii)
-    dtm->language = config_layer->Get(Config::SYSCONF_LANGUAGE);
+    dtm->language = Config::Get(Config::SYSCONF_LANGUAGE);
   else
-    dtm->language = config_layer->Get(Config::MAIN_GC_LANGUAGE);
+    dtm->language = Config::Get(Config::MAIN_GC_LANGUAGE);
 
-  dtm->bUseXFB = config_layer->Get(Config::GFX_USE_XFB);
-  dtm->bUseRealXFB = config_layer->Get(Config::GFX_USE_REAL_XFB);
-  dtm->bEFBAccessEnable = config_layer->Get(Config::GFX_HACK_EFB_ACCESS_ENABLE);
-  dtm->bSkipEFBCopyToRam = config_layer->Get(Config::GFX_HACK_SKIP_EFB_COPY_TO_RAM);
-  dtm->bEFBEmulateFormatChanges = config_layer->Get(Config::GFX_HACK_EFB_EMULATE_FORMAT_CHANGES);
+  dtm->bUseXFB = Config::Get(Config::GFX_USE_XFB);
+  dtm->bUseRealXFB = Config::Get(Config::GFX_USE_REAL_XFB);
+  dtm->bEFBAccessEnable = Config::Get(Config::GFX_HACK_EFB_ACCESS_ENABLE);
+  dtm->bSkipEFBCopyToRam = Config::Get(Config::GFX_HACK_SKIP_EFB_COPY_TO_RAM);
+  dtm->bEFBEmulateFormatChanges = Config::Get(Config::GFX_HACK_EFB_EMULATE_FORMAT_CHANGES);
 
   // This never used the regular config
   dtm->bSkipIdle = true;

diff --git a/Source/Core/Core/ConfigLoaders/MovieConfigLoader.h b/Source/Core/Core/ConfigLoaders/MovieConfigLoader.h
@@ -30,6 +30,6 @@ class MovieConfigLayerLoader final : public Config::ConfigLayerLoader
   Movie::DTMHeader* m_header;
 };
 
-void SaveToDTM(Config::Layer* layer, Movie::DTMHeader* header);
+void SaveToDTM(Movie::DTMHeader* header);
 std::unique_ptr<Config::ConfigLayerLoader> GenerateMovieConfigLoader(Movie::DTMHeader* header);
 }
diff --git a/Source/Core/Core/ConfigLoaders/NetPlayConfigLoader.cpp b/Source/Core/Core/ConfigLoaders/NetPlayConfigLoader.cpp
@@ -7,6 +7,7 @@
 #include <memory>
 
 #include "Common/Config/Config.h"
+#include "Core/Config/MainSettings.h"
 #include "Core/Config/SYSCONFSettings.h"
 #include "Core/NetPlayProto.h"
 
@@ -20,29 +21,26 @@ class NetPlayConfigLayerLoader final : public Config::ConfigLayerLoader
   {
   }
 
-  void Load(Config::Layer* config_layer) override
+  void Load(Config::Layer* layer) override
   {
-    Config::Section* core = config_layer->GetOrCreateSection(Config::System::Main, "Core");
-    Config::Section* dsp = config_layer->GetOrCreateSection(Config::System::Main, "DSP");
-
-    core->Set("CPUThread", m_settings.m_CPUthread);
-    core->Set("CPUCore", m_settings.m_CPUcore);
-    core->Set("SelectedLanguage", m_settings.m_SelectedLanguage);
-    core->Set("OverrideGCLang", m_settings.m_OverrideGCLanguage);
-    core->Set("DSPHLE", m_settings.m_DSPHLE);
-    core->Set("OverclockEnable", m_settings.m_OCEnable);
-    core->Set("Overclock", m_settings.m_OCFactor);
-    core->Set("SlotA", m_settings.m_EXIDevice[0]);
-    core->Set("SlotB", m_settings.m_EXIDevice[1]);
-    core->Set("EnableSaving", m_settings.m_WriteToMemcard);
-
-    dsp->Set("EnableJIT", m_settings.m_DSPEnableJIT);
-
-    config_layer->Set(Config::SYSCONF_PROGRESSIVE_SCAN, m_settings.m_ProgressiveScan);
-    config_layer->Set(Config::SYSCONF_PAL60, m_settings.m_PAL60);
+    layer->Set(Config::MAIN_CPU_THREAD, m_settings.m_CPUthread);
+    layer->Set(Config::MAIN_CPU_CORE, m_settings.m_CPUcore);
+    layer->Set(Config::MAIN_GC_LANGUAGE, m_settings.m_SelectedLanguage);
+    layer->Set(Config::MAIN_OVERRIDE_GC_LANGUAGE, m_settings.m_OverrideGCLanguage);
+    layer->Set(Config::MAIN_DSP_HLE, m_settings.m_DSPHLE);
+    layer->Set(Config::MAIN_OVERCLOCK_ENABLE, m_settings.m_OCEnable);
+    layer->Set(Config::MAIN_OVERCLOCK, m_settings.m_OCFactor);
+    layer->Set(Config::MAIN_SLOT_A, static_cast<int>(m_settings.m_EXIDevice[0]));
+    layer->Set(Config::MAIN_SLOT_B, static_cast<int>(m_settings.m_EXIDevice[1]));
+    layer->Set(Config::MAIN_WII_SD_CARD_WRITABLE, m_settings.m_WriteToMemcard);
+
+    layer->Set(Config::MAIN_DSP_JIT, m_settings.m_DSPEnableJIT);
+
+    layer->Set(Config::SYSCONF_PROGRESSIVE_SCAN, m_settings.m_ProgressiveScan);
+    layer->Set(Config::SYSCONF_PAL60, m_settings.m_PAL60);
   }
 
-  void Save(Config::Layer* config_layer) override
+  void Save(Config::Layer* layer) override
   {
     // Do Nothing
   }

diff --git a/Source/Core/Core/Movie.cpp b/Source/Core/Core/Movie.cpp
@@ -1306,7 +1306,7 @@ void SaveRecording(const std::string& filename)
   header.recordingStartTime = s_recordingStartTime;
 
   header.bSaveConfig = true;
-  ConfigLoaders::SaveToDTM(Config::GetLayer(Config::LayerType::Meta), &header);
+  ConfigLoaders::SaveToDTM(&header);
   header.memcards = s_memcards;
   header.bClearSave = s_bClearSave;
   header.bNetPlay = s_bNetPlay;

diff --git a/Source/Core/UICommon/CommandLineParse.cpp b/Source/Core/UICommon/CommandLineParse.cpp
@@ -10,7 +10,9 @@
 #include <OptionParser.h>
 
 #include "Common/Config/Config.h"
+#include "Common/StringUtil.h"
 #include "Common/Version.h"
+#include "Core/Config/MainSettings.h"
 #include "UICommon/CommandLineParse.h"
 
 namespace CommandLineParse
@@ -23,42 +25,41 @@ class CommandLineConfigLayerLoader final : public Config::ConfigLayerLoader
       : ConfigLayerLoader(Config::LayerType::CommandLine)
   {
     if (video_backend.size())
-      m_values.emplace_back(std::make_tuple("Dolphin", "Core", "GFXBackend", video_backend));
+      m_values.emplace_back(std::make_tuple(Config::MAIN_GFX_BACKEND.location, video_backend));
 
     if (audio_backend.size())
       m_values.emplace_back(
-          std::make_tuple("Dolphin", "Core", "DSPHLE", audio_backend == "HLE" ? "True" : "False"));
+          std::make_tuple(Config::MAIN_DSP_HLE.location, StringFromBool(audio_backend == "HLE")));
 
     // Arguments are in the format of <System>.<Section>.<Key>=Value
     for (const auto& arg : args)
     {
       std::istringstream buffer(arg);
-      std::string system, section, key, value;
-      std::getline(buffer, system, '.');
+      std::string system_str, section, key, value;
+      std::getline(buffer, system_str, '.');
       std::getline(buffer, section, '.');
       std::getline(buffer, key, '=');
       std::getline(buffer, value, '=');
-      m_values.emplace_back(std::make_tuple(system, section, key, value));
+      Config::System system = Config::GetSystemFromName(system_str);
+      m_values.emplace_back(std::make_tuple(Config::ConfigLocation{system, section, key}, value));
     }
   }
 
-  void Load(Config::Layer* config_layer) override
+  void Load(Config::Layer* layer) override
   {
     for (auto& value : m_values)
     {
-      Config::Section* section = config_layer->GetOrCreateSection(
-          Config::GetSystemFromName(std::get<0>(value)), std::get<1>(value));
-      section->Set(std::get<2>(value), std::get<3>(value));
+      layer->Set(std::get<0>(value), std::get<1>(value));
     }
   }
 
-  void Save(Config::Layer* config_layer) override
+  void Save(Config::Layer* layer) override
   {
     // Save Nothing
   }
 
 private:
-  std::list<std::tuple<std::string, std::string, std::string, std::string>> m_values;
+  std::list<std::tuple<Config::ConfigLocation, std::string>> m_values;
 };
 
 std::unique_ptr<optparse::OptionParser> CreateParser(ParserOptions options)