Thanks for all your help radatats! I've almost got everything working properly. (I used the Stomp setting on the FX send)
Here's my last problem:
I created a new patch which just has a volume pedal, red compressor, and FX Loop (set to 100% mix). I also set the patch to switch my Variax to Acoustic-3. Works amazingly.
The problem is when I switch patches, the Variax model switches off (which is the behavior I want) and everything is great, but then when I switch BACK to the Acoustic patch, the Acoustic-3 model comes back on, but the FX Loop is no longer working, even though according to HD Pro Edit, it is still enabled. Even switching the FX Loop off and back on in HD Pro Edit does not do anything, the sound just keeps coming out of the Mesa amp (my primary amp).