You shouldn't really have any major issues with this - but remember - if this is your first time installing FBA - then install it - first let it run - it should create an XML file then in the USRDIR directory. You need to look at that XML file and see the ROM path it's pointing to (you can also change this if you want). The ROM path it's pointing to needs to be the same as the one in Multiman's INI file (for FBA).
At the moment - you can't launch FBA ROMs from the File Manager - only with the Retro tab. IMO this sucks and we should b e able to launch them from the File Manager in some way - one way to solve this would be that if you were to execute a ZIP file by pressing the X button in the File Manager - it would quickly open the ZIP file and check the first file in the ZIP. If the ZIP file has a SFC/SMC/whatever file in it, then we know it's a SNES ROM - if not, it's FBA. The same could be done for all other emulators that support ZIP files (SNES9x, Genesis Plus, FCEU).