Hotkey+x will open the retroarch menu while youre in game. Then go to controls and remap as you like and then you can save it as a core remap. Remapping here won't influence your mappings in the standalone emulator because it doesn't use the retroarch controls.
On this Emulator the game dont start on my Pi. Because of this i Change to rice there the game Work fine.
What parameters you set on Mupen64auto?
Can i put the safefile from Other Emu on the mupen64