How can I stop my bunny from going to the bathroom in his sleeping room?

We have a new rabbit. The outside hutch he is in has a separate enclosed room with a solid floor for him to go into to get out of the weather, sun, etc., and a larger section with a wire floor, which is where the food and water is. However, he chooses the enclosed room as his potty area. Is there any way for me to encourage him to do his business on the side where the wire is. He doesn't go in the sleeping area for anything else, which is OK now, as it is spring. However, come winter and storms is my concern. I sc it out everyday, but haven't used a cleaner yet. I thought about vinegar, because I've heard rabbits don't like the smell of vinegar, but would he stop going in all together if I used vinegar. I thought about temporarily closing off the room in order to force him to use a new spot, and leave it that way until he's out of the habit, but wasn't sure of that would work either. Has he already "marked" his territory and that's just the way it's going to be?