Don’t worry. I figured it out:
What you need to do is replace the pifba binary with one that has 2p keyboard enabled.
Easiest way to do this is to gain root, then use WinSCP to copy the file over and change permissions.
In order to do that, remotely connect to the pi via PuTTY then put in this line:
sudo passwd root
Then set the password to something you remember like “raspberry”
Once you do that, fire up WinSCP and change your login to root and then the new password.
Navigate to the /opt/retropie/emulators/pifba folder
Now download the patched binary from a pifba fork like in this link:
https://github.com/ian57/Raspicade-configuration-files/blob/master/pifba/fba2x
Rename the old fba2x file to something like fba2x.backup and then copy the binary you just downloaded over (which you can do now since you are in root).
Now the final step is to right click the new fba2x binary, go to properties, and change the permissions. You want to click all the X boxes so they have a tick in them. Press OK and now change keyboard keys in the fba2x.cfg file (located at: /opt/retropie/configs/fba/) to whatever you have them programmed as on your IPAC, using this link as a guide:
http://www.libsdl.org/release/SDL-1.2.15/include/SDL_keysym.h
And save it, then launch pifba and voila: 2p keyboard controls work!
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