Welcome to the forum and AM,
I have only been here for three to four weeks now, and like you I was a total newbie having jumped ship from CoinOps to here, so far I am glad that I made the jump as I can get things done much faster than I could on CO, by using filters, xml files, catver and nplayers.ini.
Once you get the feel for setting up one system, then pretty much all the rest are the same on setting up, the wiki is a good place to go to, as it gives you filter information, even how to write your own skin. AM has a reasonably steepish learning curve, but as you have used GE, that reasonably looks similar in what it can do, if you do get stuck, I can always do video tutorials to help you out, as it only take a few minutes just to record setting something up, no need for fancy video editing.
It would help if you said what roms you are talking about, if it is MAME roms you can already filter these out
You need a filter and have something like this in
rule Status equals good|imperfect
You also need to make sure that you have MAME.XML or some use list.xml and catver.ini
However, you are better off just spending a bit of time and slowly clearing out the junk from your ROMS folder, create another directory called bad roms and keep them to one side, as in the future those roms may get full emulation. I played a game of Tetris last night and the warning came up that it was not perfect might have issues etc etc, but I played it and it seemed fine to me.
You do have MAME tool kits to remove clones and stuff like that if you want to do a google search for Don's HyperTools I do have the files on one of my hard drives so if you are stuck then I can hook you up with them
Regards
Mark