Run this in Mathematica:
newest = URLFetch@"https://raw.github.com/Tyilo/Mathematica-init.m/master/init.m";
initPath = ToFileName[{$UserBaseDirectory, "Kernel"}, "init.m"];
WriteString[f = OpenWrite@initPath, newest];
Close@f;
Once you have the init file installed, you can call the function updateInitFile[] to update the init.m file to the latest version.
View this imgur album for seeing the changes that I've made to the default Preferences in Mathematica: http://imgur.com/a/ko9A4