Using a frequency analyzer helps. It'll let you get in the ballpark of both amps complimenting each other real quick. Just cut one where the other is boosting, to start. One of the best guitar tones I've ever heard both live and on album was Joe Bonamassa, and he used multiple amps going into the same cab. Just an idea. I know guys like Brad Paisley will play through multiple of the SAME amp to get a fuller sound, because he swears they all sound different and they fill in different overtones, even though they're the same thing. I don't know how the Axe Fx reproduces this, so I'm not sure if that's an option you could go for. Shit man, you could get drastically different tones by having the exact same amp and cab settings but different mic positions, so... experiment!
But before I forget, one other thing to keep in mind: having one amp bone clean and another massively distorted gives you snarling brutality AND angelic clarity all at once...