Sure you can - just assign the Amp to any footswitch, like you would an FX model. The associated footswitch on the MkII will toggle the amp on/off.

There's a couple of ways to go about this, and making it work perfectly is a little more in depth than "turning an amp on and off." 

For starters, assign both amps to the same footswitch, then set the default of the patch to have one amp on and one amp off.  Pressing the footswitch will toggle both at the same time - turning one on while simultaneously turning the other off.

Then there's the issue of the raw guitar signal still being sent through the off amp.  You have a few options:

one, as hurgnanico suggested, put a volume pedal set to 0 immediatly after each amp, and set them to the same footswitch as the amps, also one turned on and one turned off. 

Alternatively, scratch all the footswitches discussed here, and set the volume on the pedals to be controlled by an expression pedal.  Set one volume pedal so that Max=100% and Min=0%, and the other that Max=0% and Min=100%.  The pedal will then crossfade between the two amps.  In this setup, both amps should turned on. 

My two cents worth, you're trying to reinvent the wheel.  Dual tone patches eat up alot of DSP, and if you're only going to run one amp at a time, you are better served with seperate patches.  Still, if this is what works for you live, I hope the above advice helps.  Happy tone hunting.