Ok this is very trivial question, but just cannot find answer anywhere.
I know there must be a JSON file with all the build systems somewhere, but I just cannot find
As dbw said, basically you should make a copy of default setting file to your User folder and edit it to override default one. And on ST3 most default setting files are packaged, use PackageResourceView will make your work easier.
For example edit default ST3 python buid setting on Windows: