The problem I ran into tonight, with importing the MAME set to test, is that when you ignore clones you can't import a few important ones manually after your initial import if you have a merged set. Example is Pacman... you import the set with no clones... when you go to import the single game manually there's no way to do it because the MAME importer wants you to add a whole folder and the rom importer can't pick out the clone because it's merged with puckman.
*edit* Also... on a side note, when I run Centipede, I get an error for missing files, but if I run the parent directly from MAMEui, it runs ok. Not sure if maybe the wrong version got imported?