So here’s my problem in detail:
https://github.com/retropie/RetroPie-Setup/issues/158

According to them, there are two options:

1) Switch the default EmulationStation emulator for SNES
2) Make an update to the ppu.cpp file and correct the code so it works with both joypads.

I’d rather do option #2, but nobody who has described that process did so with the beginner Linux user in mind. They simply say things like “edit that file<‘ when 1) I can’t even find the damn thing, and 2) I’m assuming I won’t be able to edit it with Notepad.

Help.