M/S-recording + edits:
If recording i.e. a vocalist with M/S technique (to get that little air around) which I often do, record it to a stereo track (M = left/S = right) instead of two individual tracks. Mix6To2 or Voxengo MSED get you decoded in a second.
That way you can apply i.e. VariAudio + Warp to both channels while avoiding phase issues.
Works exactly the same if you track a DI guitar + an amp, up to 6 channels, see Rhino’s tip on multitrack wave editing somewhere above in this thread.