erm, you may not need to reformat your card every time. i have been doing this too and i think you can just delete all of the folders/files and then start over again

i would also recommend that you SSH over ethernet if you can, it would be a lot easier

get yourself the FBA-libretro, not the regular FBA. this one will read the controller config file that you “Register RetroArch Controller” with

EDIT: i would like to mention that i have gotten FBA (both versions) to work with multiple controllers so it is possible. just give it another go