Yeah, just to be safe you should setup windows (if you haven't already that is) using a regular PC monitor. Once you are satisfied with it, right click on the desktop, go to 'properties', go to 'settings' tab, click 'advanced', go to the 'adapter' tab, click 'list all modes'. Then you can select 640x480 (which is hidden by default in Windows). Power down the PC, plug in your arcade monitor to the VGA port, restart and you should be all set.
If you later decide to pursue CGA arcade resolutions, you'll then want either an ArcadeVGA or Soft15khz.