Basically what you describe is correct—track 1 (input 1) would be the completely dry DI, track 2 (input 2) would be the mic signal, which would be a more ambient version of the same signal. With bass these are often mixed together, but with acoustic guitar the mic signal is almost always preferable. (Btw, technically, if you're recording a DI and a mic signal from the same source what you're doing is not stereo recording, it's two independent mono recordings.)
If for some reason you can't achieve a good-sounding mic signal (inexpensive/inadequate mic, problematic environment) then a DI'd acoustic guitar signal could potentially add some clarity and presence, but on its own an acoustic guitar DI is usually way too dry and dead, sometimes with exaggerated attacks, and it rarely will provide a suitably full, open, and natural acoustic guitar sound by itself. Mixed in with a more ambient mic signal, it might help compensate for an overly room-y mic signal, but I'd try to get a clean, usable sound from the mic alone, and then only mix in a little of the DI if the mic signal just can't cut it.
That said, if acoustic guitar is an important element in your recordings, it would be worth spending time working with the mic to achieve better sound, or even investing in a better mic (if that's the limiting factor)—good condenser mics suitable for recording acoustic guitar can be had for as little as around $100 or so nowadays, and should be capable of delivering excellent acoustic guitar recordings with a little practice. :-)