Nope, you just have to back out to the menu, turn off the controller you were using (or unplug it) and then plug the new instrument in. You only get into trouble if you try plugging one in before you've disconnected the other.

Interesting. All I have to do is go back to the main menu and use whichever instrument I want to navigate the menus. This is with both the guitar and the drums connected on the PS2 version.

Things are slightly different on the 360 purely because the signed in profile (the one associated with your gamertag, achievements, save games, Xbox Live, etc) gets tied to one of the player slots. So if you're connected and signed in on slot 1 and then start using a controller on slot 2 it won't be associated with the right profile. So you can either sign out on slot 1 and re-sign in on slot 2, or you can get it so the new controller is picked up on the same slot (if any of that makes sense).

That makes sense. I hadn't thought about just signing out the first controller.

Oh snap, a fellow PS3 RB2 owner.

LET'S BE FRIENDS.