It might help to specify what controller you are using and which emulators as some will have retroarch configs and some will be emulator specific. For a regular USB controller see this page and linked videos to get an idea of controllers.

https://github.com/retropie/RetroPie-Setup/wiki/RetroArch-Configuration

If you are using an original SNES controller with gpio pins it might be worth looking into petrockblogs controlblock

ControlBlock: Power Switch, Game Controllers, and I/O for the Raspberry Pi