Playing him on the right could work wonders. Against Atletico he usually has 2-3 players marking him in the middle whenever he receives the ball. If he's played on the right he should be able to lure more players out of position and create a lot of width and space in the middle that Iniesta, Cesc and Xavi should be able to exploit. For instance I can see Neymar getting more passing options through the middle on to his left flank as a result, and perhaps get into similar goalscoring positions like his goal in the first game.
Playing Messi in the middle against Atletico basically kind of works more to their advantage than to ours as they want to clog up the middle anyway. Not only do we strengthen their defence by playing him in the middle, but we also disable our offence in the process, leaving Messi with the thankless task of dealing with 2-3 defenders in his back, and once he shakes them off there is still the final wall of defenders...
I hope he's on fire and that whatever tactic Martino has planned works brilliantly!