Okay, I've gotten things working a bit better. I found an old VGA cord off of an old dead monitor, and I hacked it into a cable for my monitor (with separate h and v syncs). Once I did this I bypassed the video amp with this cord. Then I was able to get both guns hooked up, without the screen "wigging out" on me. Thanks for all of your suggestions.
However, the guns still aren't working great. After calibrating the guns, I found that the cursor was moving quite far from where I was aiming, making it impossible to hit anything. It was almost a random point on the screen (not VERY accurate). Sometimes the mouse cursor would move consistentally to the far upper right of the screen, after calibrating (a failed calibration?).
Any ideas?
*Edit*
I should also mention I tried calibrating in 640x480 60Hz. I played around some with 640x288 & 640x240 with no luck as well, but I might not have had the refresh set properly on those. For some reason, every time I change resolutions using that tool that came on the Ultimarc CD, it sets the refresh rate to 200Hz. I don't know if that even matters as the ArcadeVGA limits this to 15Hz anyway from what I understand.