I had some "fun" with having both a VGA and DVI output on the ATI Radeon X1600 Pro. Basically, I had my LCD monitor plugged into the DVI slot, and Arcade Monitor connected to the VGA port, via an Ultimarc JPAC. The odd thing was, once I got the arcade monitor all dialed in with soft15k and life being good, as soon as I unplugged the LCD, the arcade monitor would crap out. Connected the DVI port to the arcade monitor using a gender bender and DVI to VGA cable. Chose that route vs. uninstalling drivers, reinstalling, etc..
Groovymame is awesome on that, but if I choose a really low res game, exit that game, which goes to the selection menu, the resolution seems to stay low, so making out the letters is tough. I am hoping that using a front end will eliminate that.