I would keep him in his cage for s little bit. Work with him on the litter box before letting him out without being watched. Can you explain your litter box situation with me? I might be able to help.

Sounds like a smell issue to me. If the floor smells like urine and the litter box does not than your bun will go where he smells the urine. What I would do is thoroughly clean the spots on the floor that he likes to pee on and put a urine soaked paper towel in the litter box, under the litter to entice him to want to go there. I would also put his hay in the litter box. Rabbits like to eat and poop/pee at the same time so putting his hay in his litter box might be just enought to get him to go in it. Another thing that could be causing the litter box issues is he may be getting to much freedom. I would give him a few hours a night of supervised play time, that way when/if he does pee out of the litter box you can catch him, preferably right before or as he is peeing on the floor and pick him up and place him directly in the litter box. Then close the cage door and do not open it until he goes. This way you create a new habit so that when he has to go he hops into the litter box instead of peeing on your floors. It also gives him a consequence for his actions. He will eventually learn that peeing on your floor equals he goes in the cage and gets shut in, which he probably doesnt like. Once he is fully potty trained you can give him that freedom, but until then stick to a few hours a night when you can be home to supervise him.
Hope this helps. Keep us updated!