Geoff, One problem with powering both up is that most tube amps need to be connected to the speakers when they are powered up- be careful you don't damage the amp.
Identifying how amps differ in any aspect using a method of constant changing is fine, however if your not careful you might miss something detrimental in the sound because you are too focused. In any event, I recommend that after you do your short term comparison just relax and listen to one amp for a few days as much as you can, then take it out, plug in the other and see if you feel you are missing anything. I find this works best for me on most components and tweeks....its sort of an intuitive reaction but it usually stands the test of time.
Identifying how amps differ in any aspect using a method of constant changing is fine, however if your not careful you might miss something detrimental in the sound because you are too focused. In any event, I recommend that after you do your short term comparison just relax and listen to one amp for a few days as much as you can, then take it out, plug in the other and see if you feel you are missing anything. I find this works best for me on most components and tweeks....its sort of an intuitive reaction but it usually stands the test of time.