If you are recording one track with the mic and one track direct in, concider this:
Electricity moves faster than sound, so your direct input hits Pro Tools a little bit sooner than the miced signal. When played back together they are so close in time but off enough to cause weird frequency cancellations and funky sound.
Also- concider your playing. If your 2 parts aren' played well together (in time, in tune) almost no amount of mixing will make them blend.
Another idea: most guitarists like a full, bassy sound. Trouble is, when you start layering that sound (or adding other instruments) the excessive low end tunrs to MUD and clutters up the mix fast. This is worse on regular speakers, too, becuase they tend to emphasize the lows. Try sccoping out some 200-500hz on your guitars and see what that does. Also cut everything below 60hz.
Just some ideas.
Take care.
Chris