For RetroPie 3 beta 4, you just use the roms/fba folder – and press x as the game starts to make sure you choose lr-fba (as opposed to pifba).
Sounds like you are sorted now though.
Here is the full list of games that will work with fba-libretro
https://github.com/libretro/fba-libretro/blob/master/svn-current/trunk/gamelist.txt
