I love comping. It saves me a ton of time and heartache.
 
I have a new project coming up, and I want to put two mics on an acoustic guitar.
 
What is the best tactic to record both mics, over and over into multiple lanes, and still be able to comp each take ... while also being able to eventually separate the two signals during mixing and tweak them separately?
 
(my alleged mind thinks it might do to put the two inputs to left/right in stereo track and split the comped track later, but I can't see how to get those separate signals combined into a track)

I find one mic is fine for coming... as long as I'm facing it.
 

I had exactly the same conundrum a few weeks ago, and I can't remember what I did which isn't very helpful. I do remember that I had already recorded the comps by the time I thought - "How the hell is this going to work?" I think recording as a single stereo track then comping then splitting to two mono tracks is probably your best bet, but I'm sure there must be a better solution - I mean what if you were comping a drum kit with ten mics on 10 tracks?

Here we go I found my thread asking the same question. It seems grouping is the way - thread here

In order to have complete control over multi takes of 2 different mic's your going to have to use 2 separate tracks.
Then comp them together once recording is complete.
 
Just watch out for phase issues using 2 different microphones at the same time.

Go into preferences/record and set the option to either "always group clips" or "only group clips in folders" (and then put both tracks in a folder prior to recording). Your recorded clips will then be linked to one another and comping one will also comp the other. If you want you can eventually ungroup them.

You might try recording them in stereo L+R, and once the comping is complete, you can then go separate/export each channel separately. That's a thought, although I'd always recommend separate tracks for each mic.

I suspect you are doing this to get a wide sound.  I might suggest a different approach.  Instead of mic'ing your guitar with two mics and getting a duplicate track to pan left and right, you record two separate performances.  You will sound much wider and fuller that way.

Sanderxpander
Go into preferences/record and set the option to either "always group clips" or "only group clips in folders" (and then put both tracks in a folder prior to recording). Your recorded clips will then be linked to one another and comping one will also comp the other. If you want you can eventually ungroup them.

 
If only i had read this earlier hahaha!!  Thanks!

https://www.youtube.com/watch?v=F-_xkBoAuJw    I love this vid hes great - and he uses sonar too~