well, from what I gather, this romsorter app is really for console roms, not mame, so there should be no worries about parent roms, since on consoles one rom = one game, so there are no dependencies (well, maybe the system BIOS, but that's a different thing altogether)
for mame stuff, I suggest clrmamepro utility, which you can have re-work your collection so that each game has every file it needs right in the zip itself. Yes, it takes up a lot more space this way, but space is dead cheap, and the ease of adding/deleting games is so much nicer.
then of course, you should use ROMLister as mentioned at the top of this thread, to sort out all the games that are actually playable on your mame machine. For example, if you don't have a trackball on your machine, why put roms that need a trackball on it? ROMLister helps with that sorta stuff.
-jeff!