I figured out how to change button mapping for each emulator: While in a game in that emulator, press hotkey+B to access Retroarch config. Remap the buttons here (changing Y to B and B to A, etc.). Save to a new config file (the path where it is saved will be displayed briefly). Edit recalbox.conf adding a line for the emulator/config file you just created (example: nes.configfile=/path/to/my/configfile.cfg). Now, when that emulator is started, the cfg file with your custom button mappings will be loaded.
