If anyone else has this problem, it seems that InputAutoCfg.ini is what you are supposed to edit. Changing plugged to false just gave a no controller message. Since I didnt see any section for order, I changed the order of the controller configs but that didnt change anything. However just deleting the nes gamepad section worked and now my bluetooth controller is controller 1. It also stayed that way through restarting.

If the emulator itself doesn't implement bezels, then there's not much that can be done to externally overlay an image, since most emulators need exclusive/fullscreen access to the video output.