I'm about to dig into recording direct with the AFX, but this applies to any setup, really.
As I understand it, I run a dry signal into my bus, then route it out through a bus with (amp_model_whatever) on it. So the signal coming into my software (say, Reaper) is essentially clean and gainless, and the gain is added after the fact, correct?
Then if I want to play something once, and hear it with a few different amp models, I just change the amp model and the signal path stays the same?
That's the general idea. A lot depends on your recording platform and hardware.
There are a lot of ways to use reamping with the Axe Fx. I do all the reamping inside my Axe Fx.