Hey Mike, what are you trying to do exactly?
I am not sure I fully understand, but I think phase aligned means keep the phase on each mic the same. IE don't reverse the phase on one mic. But again it would helpful if you could fill in more details

if the sound does not reach the mics at the SAME time, it can cause phase misalignment ...which can cancel out certain frequencies. the phase align rule of thumb, while not perfect, is 3 to 1, meaning the second mic should be 3 times as far from the source than the first mic is. if the mic are both, say 3 inches from the sound source ...they will be phase aligned.

Hold on there- There's a bit of misinformation here.
Let's start with LINK555
- Hitting the phase button will reverse the polarity of the mic, which is what you were referring to, but that puts it exactly 180 degrees out of phase (technically it's still not out of phase but that's another story) The mics can have the same polarity but still be out of phase- Read on, and I'll explain.

TheBlueRoom-
You're much closer, but in this case it's much more complicated than that.

The 3 to 1 rule applies to the distance between 2 (or more) mics. (not the distance from the mics to their target)
So if Mic #1 is 3 inches from speaker #1 then there should be no other mic within at least 9 inches of that mic.

This shouldn't be a problem with a gtr amp that has at least 10" speakers. They will be far enought apart in the cab for this to work as long as your mics are less than 4" from the speaker.

However, in this case we're not talking about a single sound source. We've added a 2nd speaker, so we now have 2 sound sources and 2 mics. So naturally, some of the sound from speaker #1 is going to find it's way into Mic #2 and vice versa.

In a perfect world TheBlueRoom is correct, keep both mics the same distance from the speakers. (while at the same time observing the 3 to 1 rule between mics- So in other words don't mic the left speaker to the right of center and the right speaker left of center as this might put the 2 mics too close together. This would be much easier with a diagram)

But there's no guarantee that the 2 speakers would react the same. (guitarist have been known to replace blown speakers with types that don't match the others in the cab. Speakers change over time, and home made wiring schemes can wreck havoc on engineers)

So here's how you test your setup:
- Mic the speakers the way TheBlueRoom suggested (3" from each speaker)
- Bring these up on 2 channels. Pan both to center. But keep the volume of mic #2 down.
- Now, slowly bring up the vol of mic#2.
- You should only hear a change in volume and if you're lucky a favorable improvement in tone. If you hear an adverse change in tone,like it gets too thin or boomy, or hollow, then you need to slightly adjust the mic either a tad closer or further. Also pointing at the center or off center of the speaker cone can change things.

Now- having said all that, I think for the beginning engineer, it might be best to perfect the single mic setup first, before attempting more complicated advanced setups.

Now- onto your other questions.
- Yes, PA mic pres can work. But there's no guarantee that they will be 'Good' pres. (as always, some mixers sound better than others)
- Direct outs might be ok if you're doing a very clean jazzy style of recording. (or if you're using some amp modeling gizmo) Otherwise it's best to mic the cab.
- Stereo- there's no rules. You might want to start by recreating the live stage setup. Maybe one guitarist stage left, the other stage right, etc.

Ok-I've rambled on way too long.

to clarify, I did mean they should be on the same speaker, not necessarily two different speakers on the same cab ...but, nice clarification on the 3 to 1 rule ...I've always done it the other way with good results ...luck?

Actually, I don't see the point of putting two identical mics on two indentical speakers. (or even 1 speaker)
Seems somewhat redundant and asking for trouble.
I've used different mics on the same speaker, and I've used different mics on multiple speakers within the same cab.

The only purpose of using a matched pair of mics would be for some stereo purpose. But in the case of "Mikeguitar1" original question there is no stereo sound produced.

TheBlueRoom- yeah, it's pretty easy to follow the 3 to 1 rule without even trying. As long as you're close micing, it's rare that you'll have two mics that close together.
It becomes more of an issue as you move the mics further from the source. So say, if you have 2 vocalists that are a foot away from their mic, (2 mics- one on each vocalist) then the 2 vocalists should be at least 3 feet away from each other.