When Using 2 mics...

There is no rule, but if you are not sure record in different tracks!

Personally if I use more than one mic for one take, I do in this way so in the mix I can balance them better if I need.

One of the reason of using more than one mic is to have different flavors, for example a clearer and a darker sound so in the mix time if you need the clear one more, it's enough to raise the level of that one!

Pay attention to phase issue and assure that the distance between the two mics and the speaker is the same (if you want to record the ambient is another thing!!).

Record also the line if you can in case of reamp!

Then reapeat for other 3 takes
 
I do 2 takes per side no matter how many mics I'm using. When I'm recording the mics as I go, I'm limited to 2 mics, since my Mbox only has 2 inputs. :p However, I have to remind myself not to go crazy with impulses, since I can blend so many more mics at a time. Really, though, whatever blend and balance of mics sounds the best to me, I use it for all the main rhythm takes for a consistent, thick sound. I'll usually move the mic or mic a different speaker for leads just so it stands out... makes much more of a difference than messing with the amp, in my opinion.