Was working with a friend to setup a special configuration for FBA so that you can change the mapping of the controllers differently for each ROM. What I was able to do was add the following code to the runcommand.sh file:
if [ $system = "fba" ]; then
echo "FBA, Looking for ROM specific config"
if [ -f "$rom.cfg" ]; then
echo "SPECIAL ROM CONFIG FOUND"
sudo ln -f -s $rom.cfg /opt/retropie/emulators/pifba/fba2x.cfg
fi
fi
# run command
eval $command </dev/tty 2>/tmp/runcommand.log
if [ $system = "fba" ]; then
sudo ln -f -s /home/pi/RetroPie/roms/fba2x.cfg /opt/retropie/emulators/pifba/fba2x.cfg
fi
Once this was added, I moved fba2x.cfg to the above listed path (/home/pi/RetroPie/roms), then you just make a file that matches the rom with a .cfg extension. For each config, if it is found, it is loaded as the FBA config (controller mapping) for that game specifically.
IE: For a ROM sfa2.zip, you would make a config file sfa2.zip.cfg in the roms folder.
Hope that helps someone!