To the original poster, did you ever get this to work? I just got my 8bitdo SNES30 controller set up last night. I used the guide found at https://github.com/RetroPie/RetroPie-Setup/wiki/Setting-up-a-Bluetooth-controller.

I had the controller connect via bluetooth within about 20 minutes. That was the easy part. The trouble that I had was that the buttons seem to be different for controlling emulationstation (selecting games and systems) than for controlling the actual games.

The trick I found was that the config for emulationstation is found at /home/pi/.emulationstation/es_input.cfg and uses the button numbers you got from step 5 of the guide. For whatever reason, I was unable to program the d-pad directions, but they just worked already. The config for actual games is found in /opt/retropie/configs/all/retroarch-joypads and is created in step 6. Don’t try to use the same button numbers in the two config files or it won’t work.

I am still having trouble trying to get the shoulder buttons to work as hotkeys for loading/saving save states, but otherwise it works great. Hopefully this helps.