Personally I only ever use two amps in a multi amp setup, and that's not that common for me. When I do that I'll only be doing one mic per amp (unless it's a Leslie) because I don't need all that extra thickness. There's saturation happening between the amps. If you want perfect alignment you can print a DI while tracking with the core sound, and then run that DI through the second head plugged into the existing cab without moving the mic. Again, be wary of some heads inverting polarity.
You know, I have to say that while I love the multiple mic'd thing for certain genres and bands, as a mixer, I find it's often too much in a busier track. Like all techniques it has its place. What I'm trying to say is that you don't have to phase align, time align, multi mic, multi amp etc to get a great sound. Those techniques can be just the ticket but not always.