If you use ClrMAME you can separate your BIOS sets really easily.
First, create an empty directory. Name it 'Neo Geo' or something.
Select your .dat file (which you create from the commandline: 'mame -listinfo > mame66.dat') and go to 'Scanner'. There is a 'Systems' button there. Once you push it there will be separate directories for each BIOS type. Double click the one for Neo Geo and put the path in for the directory you just created.
Back out by clicking the 'x' in the corner, and do it again for the next window so you're back at the main menu. Select 'Rebuilder.'
Make your source your main ROMs folder and for destination click the box for SystemDefaut Paths. Smack the rebuild button. In a little bit you will have nothing in your Neo Geo directory except the Neo Geo ROMs. You can even click the 'remove rebuilt sourcefiles' if you don't want double ROMs.
You can do this for all your sets. I keep mine in their respective folders. Makes it easier, I think.