In that scenario, you could specify that they be launched with PiFBA through the Runcommand menu, but that's putting the cart before the horse right now. If there are games however that aren't on that romset but are on other romsets such as PiFBA which has the romsert FB Alpha 0.2.96.71? Do you then copy those games into your neogeo folder along with the neogeo.zip file into the bios folder or just leave it in the neogeo roms folder. My advice to you is to stick with the default lr-fbalpha and simply use the 0.2.97.43 ROM set. Of course you would need to change the ROM set accordingly if that were the case. However, RetroPie allows the option to change the default by using the Runcommand menu if you so chose.
Lr-fbalpha happens to be the default, so yes. If I then put those in the neo geo roms folder, will retropie automatically recognise that they are to be launched with lr-fbalpha so there shouldn't be further configuration. If I want to use for example lr-fbalpha for neo geo then I am limited to FB Alpha v0.2.97.43 romset so basically any roms that are contained within that collection? In this case, 'good' ROMs refer to those from a numbered set that correlates to the emulator. How do I know which ones are going to work and are 'good' as opposed to which ones aren't?