I'm sure it varies from position to position, but there is a kind of rotation. I remember reading an interview with Capt. Hans, the former captain of the Magic. I think he said that he spends 6 or 8 weeks on board, and then one of the "staff" captains takes over for a month, giving him some time on land to spend with his family. He also said that they occasionally sail with him.
In seven trips on the Magic, we've had Captains Hans, John and Henri (is it Henri? His last name is Andersson, he was interviewed on the Travel Channel special, his name escapes me right now).
There is a designated captain for each ship, and I believe there are two staff captains, which rotate in to give the others a break.