the only right answer is whatever you think sounds good... only you are the one who decides what good tone is to you.
its really that simple... setting your amp to a different tone in hopes it will sound different once recorded is... stupid. It wont happen. You can edit the hell out of it and adjust the EQ once its recorded, but pushing all the highs wont make it sound like Band X Y or Z once its recorded.
the mics will impart their own unique character... the only thing you can do is EXPERIMENT. Try it out. Record some guitar tracks, and analyze the sound. Is it too brittle? Roll back the highs a bit. Kinda muddy? Boost the mids. Not oopmh-y enough? boost the bass a bit.
PERSONALLY, what I do is boost the lows and lower mids and the highs a little bit, because that gives you the scooped-mids tonal character without ACTUALLY having the mids scooped out: they are still there, so it will cut through.
I also use a Boss EQ pedal, because amp EQ's don't do jack shit unless they're active, and afaik, only Mesa uses active EQ. It really is AMAZING what you can do with your sound when you get an EQ pedal. Its easily the most important piece of gear in my rig, and I've used it with every amp I've owned, from my old Marshall, to my 5150, and now my Carvin Belair.
also, if you want to get a better overall sound, adjust the EQ on the 2nd track, because recording a 2nd track with the EXACT same setup will result in odd phasing issues because you aren't going to be playing the exact same thing, even though the tone is the same. There will be slight timing issues, and it will muddy up the sound. Make the two tracks distinct.
I suggest starting with whatever your prefered overall tone is, and then for the 2nd track, take out a little bit of the bass and pump up the mids to give it a lot of attack and pressence, because that will blend with the oomph you'll get from the initial track to create an overall guitar tone that is both present and in your face, but still thick and fat with bottom end.
Mic placement also matters.
but seriously man, theres no right answer. the only thing you can do is experiment until you find what you like.
Try plaacing the mics directly facing the speaker cone, and then try placing it at a 45 degree angle. or do both mics at once, with one facing directly and one at a 45 degree angle. try them both on one cone, on separate cones, etc.
seriously man, i could write for hours on what you COULD do. but nothing that i write will actually give you a sonic sample of the result. you just gotta fuckin get up and do it and find out what you like. thats what makes you into a good audio engineer.