I think the frontcourt we saw at the end of the game (Marek, Guerrier, and Griffen) was our best overall, at least against most opponents. But as others have pointed out, Marek can't really play center the whole game without either fouling out or getting close to it. So Boeheim's gonna want to make sure he has his best frontcourt available at the end of the game, when he might really need them.
So that's another reason for Boeheim to at least try to get Frank and/or Jesse to absorb some of the fouls at the Center position early on, so long as it isn't too costly to the team. That will be Frank's and Jesse's best opportunities to show what they can do.
Now if one or both of them ends up doing pretty well at defending the rim, then that's a whole new discussion...