My WG D9800 does 800x600 with no flicker and no problems, this avoids the HUGE windows you get with 640x480, I highly recommend going that route. Use Soft 15khz to install all the resolutions and you are off to the races.
Agree to use a standard PC monitor to set things up, especially Soft 15khz. Also, first thing you want to do is select 800x600 @60 in the windows control panel (DISPLAY) settings. This way you can hot swap over to the WG and it will lock on. Otherwise the frequency your video card spits out is way too high for the WG. Text will never be clear like on a pc but 800x600 is fairly legible. Everything in games looks great though.
Good luck.