I just set the system up two days ago, but I was able to gather this:
1. when i am at the game station selecting page, when i press Start, there’s a “Configure Input”;
This is the controller configuration for the EmulationStation frontend (The GUI that displays all your available emulators/roms)
2. when i select RetroPie, there’s a “Configure RetreArch Kyeboard/Joystick”
This is the gamepad/keyboard configuration for the emulators that use the RetroArch/Libretro libraries. A good chunk of the emulators use it and would share controller configs.
3. same page, “Controller Configuration”
I believe this is where you’d configure a controller that does NOT use the Retroarch libraries.
Anyone else can correct my if I am wrong with these assumptions.