Bayern are good without the ball but not as good as Dortmund and Atletico IMO. They (Bayern) play a more dominant game though, so the opposition don't always get the chance to attack them.
@ Volante
Think Martinez will end up playing at CB for Bayern, probably in a role similar to the one Rijkaard played at Ajax in the mid nineties; drops to CB without the ball but moves to midfield when in possession. Bayern are playing a much higher defensive line compared to last season (and are much more dominant in the attacking 3rd), so they could do with Martinez's passing from the back. I don't think he should worry about his future at Bayern, Guardiola wanted him when he was at Barca.
I think Schweinsteiger is probably the one that should worry a bit about his future (sounds a bit ridiculous I know); he hasn't played that well so far under Guardiola IMO, and will probably be the one that would make way for Lahm if Guardiola continues using him in midfield. Kroos is the untouchable in their midfield. He's truly a special player, the closest thing to Xavi there's at the moment.