diff --git a/Source/Core/DolphinQt/MenuBar.cpp b/Source/Core/DolphinQt/MenuBar.cpp
@@ -848,105 +848,106 @@ void MenuBar::AddJITMenu()
 
   m_jit_off = m_jit->addAction(tr("JIT Off (JIT Core)"));
   m_jit_off->setCheckable(true);
-  m_jit_off->setChecked(SConfig::GetInstance().bJITOff);
+  m_jit_off->setChecked(Config::Get(Config::MAIN_DEBUG_JIT_OFF));
   connect(m_jit_off, &QAction::toggled, [this](bool enabled) {
-    SConfig::GetInstance().bJITOff = enabled;
+    Config::SetBaseOrCurrent(Config::MAIN_DEBUG_JIT_OFF, enabled);
     ClearCache();
   });
 
   m_jit_loadstore_off = m_jit->addAction(tr("JIT LoadStore Off"));
   m_jit_loadstore_off->setCheckable(true);
-  m_jit_loadstore_off->setChecked(SConfig::GetInstance().bJITLoadStoreOff);
+  m_jit_loadstore_off->setChecked(Config::Get(Config::MAIN_DEBUG_JIT_LOAD_STORE_OFF));
   connect(m_jit_loadstore_off, &QAction::toggled, [this](bool enabled) {
-    SConfig::GetInstance().bJITLoadStoreOff = enabled;
+    Config::SetBaseOrCurrent(Config::MAIN_DEBUG_JIT_LOAD_STORE_OFF, enabled);
     ClearCache();
   });
 
   m_jit_loadstore_lbzx_off = m_jit->addAction(tr("JIT LoadStore lbzx Off"));
   m_jit_loadstore_lbzx_off->setCheckable(true);
-  m_jit_loadstore_lbzx_off->setChecked(SConfig::GetInstance().bJITLoadStorelbzxOff);
+  m_jit_loadstore_lbzx_off->setChecked(Config::Get(Config::MAIN_DEBUG_JIT_LOAD_STORE_LBZX_OFF));
   connect(m_jit_loadstore_lbzx_off, &QAction::toggled, [this](bool enabled) {
-    SConfig::GetInstance().bJITLoadStorelbzxOff = enabled;
+    Config::SetBaseOrCurrent(Config::MAIN_DEBUG_JIT_LOAD_STORE_LBZX_OFF, enabled);
     ClearCache();
   });
 
   m_jit_loadstore_lxz_off = m_jit->addAction(tr("JIT LoadStore lXz Off"));
   m_jit_loadstore_lxz_off->setCheckable(true);
-  m_jit_loadstore_lxz_off->setChecked(SConfig::GetInstance().bJITLoadStorelXzOff);
+  m_jit_loadstore_lxz_off->setChecked(Config::Get(Config::MAIN_DEBUG_JIT_LOAD_STORE_LXZ_OFF));
   connect(m_jit_loadstore_lxz_off, &QAction::toggled, [this](bool enabled) {
-    SConfig::GetInstance().bJITLoadStorelXzOff = enabled;
+    Config::SetBaseOrCurrent(Config::MAIN_DEBUG_JIT_LOAD_STORE_LXZ_OFF, enabled);
     ClearCache();
   });
 
   m_jit_loadstore_lwz_off = m_jit->addAction(tr("JIT LoadStore lwz Off"));
   m_jit_loadstore_lwz_off->setCheckable(true);
-  m_jit_loadstore_lwz_off->setChecked(SConfig::GetInstance().bJITLoadStorelwzOff);
+  m_jit_loadstore_lwz_off->setChecked(Config::Get(Config::MAIN_DEBUG_JIT_LOAD_STORE_LWZ_OFF));
   connect(m_jit_loadstore_lwz_off, &QAction::toggled, [this](bool enabled) {
-    SConfig::GetInstance().bJITLoadStorelwzOff = enabled;
+    Config::SetBaseOrCurrent(Config::MAIN_DEBUG_JIT_LOAD_STORE_LWZ_OFF, enabled);
     ClearCache();
   });
 
   m_jit_loadstore_floating_off = m_jit->addAction(tr("JIT LoadStore Floating Off"));
   m_jit_loadstore_floating_off->setCheckable(true);
-  m_jit_loadstore_floating_off->setChecked(SConfig::GetInstance().bJITLoadStoreFloatingOff);
+  m_jit_loadstore_floating_off->setChecked(
+      Config::Get(Config::MAIN_DEBUG_JIT_LOAD_STORE_FLOATING_OFF));
   connect(m_jit_loadstore_floating_off, &QAction::toggled, [this](bool enabled) {
-    SConfig::GetInstance().bJITLoadStoreFloatingOff = enabled;
+    Config::SetBaseOrCurrent(Config::MAIN_DEBUG_JIT_LOAD_STORE_FLOATING_OFF, enabled);
     ClearCache();
   });
 
   m_jit_loadstore_paired_off = m_jit->addAction(tr("JIT LoadStore Paired Off"));
   m_jit_loadstore_paired_off->setCheckable(true);
-  m_jit_loadstore_paired_off->setChecked(SConfig::GetInstance().bJITLoadStorePairedOff);
+  m_jit_loadstore_paired_off->setChecked(Config::Get(Config::MAIN_DEBUG_JIT_LOAD_STORE_PAIRED_OFF));
   connect(m_jit_loadstore_paired_off, &QAction::toggled, [this](bool enabled) {
-    SConfig::GetInstance().bJITLoadStorePairedOff = enabled;
+    Config::SetBaseOrCurrent(Config::MAIN_DEBUG_JIT_LOAD_STORE_PAIRED_OFF, enabled);
     ClearCache();
   });
 
   m_jit_floatingpoint_off = m_jit->addAction(tr("JIT FloatingPoint Off"));
   m_jit_floatingpoint_off->setCheckable(true);
-  m_jit_floatingpoint_off->setChecked(SConfig::GetInstance().bJITFloatingPointOff);
+  m_jit_floatingpoint_off->setChecked(Config::Get(Config::MAIN_DEBUG_JIT_FLOATING_POINT_OFF));
   connect(m_jit_floatingpoint_off, &QAction::toggled, [this](bool enabled) {
-    SConfig::GetInstance().bJITFloatingPointOff = enabled;
+    Config::SetBaseOrCurrent(Config::MAIN_DEBUG_JIT_FLOATING_POINT_OFF, enabled);
     ClearCache();
   });
 
   m_jit_integer_off = m_jit->addAction(tr("JIT Integer Off"));
   m_jit_integer_off->setCheckable(true);
-  m_jit_integer_off->setChecked(SConfig::GetInstance().bJITIntegerOff);
+  m_jit_integer_off->setChecked(Config::Get(Config::MAIN_DEBUG_JIT_INTEGER_OFF));
   connect(m_jit_integer_off, &QAction::toggled, [this](bool enabled) {
-    SConfig::GetInstance().bJITIntegerOff = enabled;
+    Config::SetBaseOrCurrent(Config::MAIN_DEBUG_JIT_INTEGER_OFF, enabled);
     ClearCache();
   });
 
   m_jit_paired_off = m_jit->addAction(tr("JIT Paired Off"));
   m_jit_paired_off->setCheckable(true);
-  m_jit_paired_off->setChecked(SConfig::GetInstance().bJITPairedOff);
+  m_jit_paired_off->setChecked(Config::Get(Config::MAIN_DEBUG_JIT_PAIRED_OFF));
   connect(m_jit_paired_off, &QAction::toggled, [this](bool enabled) {
-    SConfig::GetInstance().bJITPairedOff = enabled;
+    Config::SetBaseOrCurrent(Config::MAIN_DEBUG_JIT_PAIRED_OFF, enabled);
     ClearCache();
   });
 
   m_jit_systemregisters_off = m_jit->addAction(tr("JIT SystemRegisters Off"));
   m_jit_systemregisters_off->setCheckable(true);
-  m_jit_systemregisters_off->setChecked(SConfig::GetInstance().bJITSystemRegistersOff);
+  m_jit_systemregisters_off->setChecked(Config::Get(Config::MAIN_DEBUG_JIT_SYSTEM_REGISTERS_OFF));
   connect(m_jit_systemregisters_off, &QAction::toggled, [this](bool enabled) {
-    SConfig::GetInstance().bJITSystemRegistersOff = enabled;
+    Config::SetBaseOrCurrent(Config::MAIN_DEBUG_JIT_SYSTEM_REGISTERS_OFF, enabled);
     ClearCache();
   });
 
   m_jit_branch_off = m_jit->addAction(tr("JIT Branch Off"));
   m_jit_branch_off->setCheckable(true);
-  m_jit_branch_off->setChecked(SConfig::GetInstance().bJITBranchOff);
+  m_jit_branch_off->setChecked(Config::Get(Config::MAIN_DEBUG_JIT_BRANCH_OFF));
   connect(m_jit_branch_off, &QAction::toggled, [this](bool enabled) {
-    SConfig::GetInstance().bJITBranchOff = enabled;
+    Config::SetBaseOrCurrent(Config::MAIN_DEBUG_JIT_BRANCH_OFF, enabled);
     ClearCache();
   });
 
   m_jit_register_cache_off = m_jit->addAction(tr("JIT Register Cache Off"));
   m_jit_register_cache_off->setCheckable(true);
-  m_jit_register_cache_off->setChecked(SConfig::GetInstance().bJITRegisterCacheOff);
+  m_jit_register_cache_off->setChecked(Config::Get(Config::MAIN_DEBUG_JIT_REGISTER_CACHE_OFF));
   connect(m_jit_register_cache_off, &QAction::toggled, [this](bool enabled) {
-    SConfig::GetInstance().bJITRegisterCacheOff = enabled;
+    Config::SetBaseOrCurrent(Config::MAIN_DEBUG_JIT_REGISTER_CACHE_OFF, enabled);
     ClearCache();
   });
 }