Can you confirm the exact directory you have put your SNES roms in?
It *must* be this for RetroArch to use them
/home/pi/RetroPie/roms/snes/
If they are in there (and not also in other folders), it should be using the retroarch config files in the same way that, for example, the Megadrive does.
Are you using 2.6.0?
