I know the thread is locked, but the answer you found James isn't exactly what you're after.
The controller directory you found contains presets for various controllers. For your controls as you've configured them yourself, you'll want to copy the controller.ini file from the same folder your .plr file is in.
The controller directory you found contains presets for various controllers. For your controls as you've configured them yourself, you'll want to copy the controller.ini file from the same folder your .plr file is in.