I'm not sure if I understand your question correctly, but one way to approach getting the right guitar sound is to have a sample of the song with drums and bass playing while you apply various guitar tones against it. Once you pick a guitar tone that you can work with, then tweak it if necessary, but only against the same sample of drums and bass.
Then when you record the track for real (assuming you havent added the bass guitar yet) leave the guitar sound as is. Reserve any judgement until the bass has been recorded. Usually you will not have to make any adjustments because you have already determined how the guitar should sound from the sample you recorded earlier.
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