Hello Mr. sheepishbacon,
I would’ve used GPIO to connect my controls but my RPi 3 is still incompatible. I have linked below to the software, it’s called ‘Porta pi’ but it’s really just retropie with GPIO support.
As for me I’ll be using the guts of a keyboard to attach the controls though I’ll probably switch to GPIO when RPi 3 is supported.
http://www.retrobuiltgames.com/porta-pi-arcade-help/porta-pi-software-os-download/