I always recommend visually (and audibly) lining up the tracks IF there's a phase issue, but I agree with jb101, you really shouldn't have so much of an issue. Having two exact copies of the same signal playing together merely brings up the apparent volume of that signal, nothing more. Having one processed will be just a lesser effect than recording only one track and processing that one track. If you flip the phase switch on one, you'll hear the bass (at least the low end) nearly disappear, and you likely don't want that. In Mono, the bass would be near-silent, since the two signals simply cancel each other out.
For tracking, I don't personally recommend going through Guitar Rig during tracking. I recommend processing through Guitar Rig after.