I always use the VG-99 as a front end into my Ultra. I only use pickup modeling, altered tunings, acoustic sims, sitar, etc. I never use the VG's amps.
I run the VG's Main Out jacks (1/4") left and right into the corresponding left and right rear number 1 inputs on the Ultra. This way, I can use the VG in "stereo" or mono. I can also set the left for an acoustic sim and the right for an electric, and process both independently in the Ultra. If you also send the Guitar Out jack of the VG into one of the Ultra's number 2 inputs, you can process the VG tones in stereo and your normal guitar indpendently at the same time, if you can give up your effects loop.
I keep the output knob on the VG at max and adjust its patches to barely light the Ultra’s meters when the Ultra input knob is set around 12 o'clock.
I've never found a need to use the COSM noise gate. I use the Ultra's gate.
My main VG patch is just a "through" for normal pickup operation. The noise it adds is negligible, even with substantial gain in the Ultra. The COSM pickups do have more hiss, but zero hum induced by external fields. The Ultra's gate works great for me. I guess I'm not "high gain" enough for the noise to be a problem.