There is no reason that you can't use these strategies even if you rotate classes.
I have mainly used the class-yes, teach-ok, some of the common procedures, and a bit of the score board, so I'm not an expert, but it is all very easy to introduce.
I even used the class-yes, and teach-ok when we rotated all of our grade level for testing review. I only had each group for less than two hours, but the kids picked up on the procedures in less than five minutes and it helped them stay engaged.
If you are wondering how to do the classroom management levels for three different classes, I'm assuming it would be pretty easy to simply have 3 small scoreboards on the white board at one time. When I was in a room with little wall space, I put alot of posters on hangers and hung them in the front of the class as needed. You might be able to do something similar for the practice cards and have one pocket chart poster for each class.
I wouldn't worry if you decide to use Whole Brain practices, and your teaching partners do not. As I said, the kids pick it up so quicly, it shouldn't be a problem.