Chipper hates the OF and prefers 3B. Don't know whether he'd try 1B, but I highly doubt he heads back to the OF since he's said several times how he feels the running required in the OF has contributed to his leg injuries the past couple of seasons.
As such, unless they trade Chipper, I can't see Marte at 3B in a Braves uniform any time in the near future.
As such, I expect a MCab type of career progression. He may stink at it intitially, but with work in winter ball and ST, my guess is that Marte is in LF next year. I think Langerhans has shown himself to be more of a 4th OF type, which leaves Kelly Johnson in RF (or traded) and Francoeur in AAA (learning how to take a BB) or in RF, if Johnson is traded. Then, when Chipper's contract is up, Marte moves to 3B.
I agree with Sultans, though, that for 2006, Encarnacion would be a better option as a 3B prospect. While Marte may end up at 3B eventually, I don't think it'll happen in 2006 making Encarnacion my choice as well.