wowzer22: Did you get it to work? I just copied my roms to the FBA-folder and it worked. The FBA-emulator uses the exact same button mapping as the my other retroarch configs. But if you copy your default retroarch.cfg and place it in your configs/fba folder and then change the buttons manually it should work.
Has anybody tried this guide with RetroPie 3.6? Or is it fixed in 3.6 so you don´t need it? Please let us know! When I get the Raspberry Pi 3 I will try it out:-)