For sure.  It's a good trick.

The basic instructions to assign an effect to a footpedal are here --> http://line6.com/support/docs/DOC-2721.   You can use these for an amp by simply selecting the Amp Model name in Step 2.

Assign both amps to the same footpedal and then turn one of them off.  Now when you hit the footpedal you should be able to swap between the amps.

Beware the channel bypass volume!  When you turn an amp off, you will still get a clean signal go down that path unless you turn this volume down.  To do this:  simply go to the amp when it is turned off in HD Edit and adjust the amp volume (the title of which should have changed from 'Volume' to 'Bypass' or similar).  Repeat for the other amp.