Do you feel it's better to have one guitarist track all of the rhythm parts and the have them each record their own leads or special licks, or do you like to have each guitarist record all of their own parts, including rhythm guitar?
If it's metal I'd go with one guy. Generally the guy that writes most of the shit. If they both write, I'd just pick the tighter guy. Simple.
There is typically one player who is better at rhythms. I would have him play all the guitar parts where they play the same part, and have the other guitarist come in for his parts ( unless he can't play them for shit ). For leads, I let the guitarists do their own thing.