Only AdvanceMAME and AdvanceMenu will let you write direct to video card modes, but they're both difficult to set up correctly, and dangerous if you pass the wrong modes to your monitor. You can potentially cause permanent damage to your monitor if you do the wrong thing!
Best bet is as Howard said, and buy an ArcadeVGA. It's literally plug and play simplicity. Along with the iPac/jPac, it's the best thing to ever hit the cab-building community.