I guess whatever works is fine. I know that's not much help. My buns have the run of the kitchen/dining room and a cage on the floor they can retreat to but the door is always open, so I have no experience. The only trouble I see is that sometimes bunnies ar threatened by a hand coming into a cage and lifting them out; it's usually better to open the door and let them come out on their own. But if your guys are used to being picked up and taken out it probably doesn't matter. Are you trying to litter train them? Any luck?