You wouldn't really do something like that would you?
If you want to some GENERAL information I've got a pretty good idea as to how things are projected to work, but this is just from what I've gathered and not supposed to be the definitive end all, be all answer.
Basically there will be a new effect block inside the AxeFXII that is called "tone matching". You will put this in the preset and then have the option of tone matching an actual amp or a recording. In order to do either though you will have to either know what the original amp model was or do your best guessing and put that amp model in the preset. So the tone matching feature will use the amps inside the AxeFXII.
If you are doing a real amp you will need to have a mic and probably a pre-amp in. That will plug into the back of the AxeFXII. (You will not plug an amp directly into the AxeFXII's rear input; that will blow your output transformer on the amp and probably take out the input circuit on the AxeFXII in the process.) This is where the actual process gets a bit fuzzy for me, but I believe that the tone matching block will 'record' your sound from the amp so you are either going to play the amp or it will send a signal to it or something. We don't have specifics on this yet. Either way it's a small issue IMHO.
After you've got the reference loaded into the tone matching block you will play your guitar into the front input (I'm assuming) and it will try to make the changes needed to match the tone. Now I've heard that you don't have to play the exact same notes, but obviously the closer you are the better it would probably work out for you. After its done you will be able to go in there and adjust parameters just like you would on any patch. You can change cabs and stuff as well.
What it won't do is capture stuff like delay or reverb so you'll have to add those after the process. It's sole purpose is to match the tone of the amp.
In order to tone match from a recording instead of using a mic and pre-amp you will be sending the audio into either the rear input or the USB port from a computer or audio device. The process should be the same, you are just using a different source for the reference.
As far as I know this is as much as any of us who aren't beta testers or named Cliff Chase know so far. I may have a few details wrong (probably likely) and what I think I might know may actually be true today and it may change tomorrow. But it's the basic process.
No amps getting plugged into your AxeFXII directly from the speaker outputs. Please don't do that.