If you're talking about the plastic thing-a-ma-bob that you place over a plate when reheating to prevent spattering, then yes it should go back inside if there is no other room for it.
Luckily, I have a typical 1980's house where they had a honker built in microwave atop of the wall oven, but it was removed long before I bought the house. I have a freestanding microwave and there's plenty of room on top for the microwave cover.
Alternatively, you could just hide it from everyone and use it only for yourself.