Hey, everyone note that AN ATI CARD worked with Advancemame. My 7000 did, too.
cw, did you run advcfg before running games? - meaning, ideally, you need to have a device_video_format line. If you just set clock values, Advancemame will try to work within the constraints it senses in your monitor, but this can be kind of loopy and can give weird results. At least you got it working, but it's good to know all how the thing works. I actually have an Advancemame tutorial for Windows lurking around (not sure if it's in the wiki...), and though some of the names are different in Linux, I'd bet the process is essentially the same.
kev: Advancemame has only one configuration file, in rc format.