In RetroPie 3, the NeoGeo roms go in
/home/pi/RetroPie/roms/neogeo
Then when you run one of the roms, press x to choose “gngeo” as the emulator (assuming thats the emulator you have the romsets for).
You only have to choose a default emulator once.
Do the same (press x) when you start a n64 rom, just to confirm you are using the right emulator.
