Not sure about FDS but for Super CD games place syscard3.pce and SYSCARD3.pce in both your BIOS folder and your roms folder. I am not sure which one it is that works, but one of them does anyway. I can only get bin + cue games to run.
Bin/cue worked.
I did have syscard3 and SYSCARD3 in the roms and bios folder so not sure which worked yet.
