I suspect your bunny is marking his territory with pee and poop! It’s wonderful that he knows to relax and eat in his litter box, now it’s just a matter of getting him to pee and poop in it too. I suspect you may have to restrict his area until he shows signs that he’s getting the hang of using his litterbox as you want him to use it. Perhaps an x-pen setup that is large enough for him to feel at home, at least 4’x8’ in area, will work? You can let him run around outside his pen when you are there to supervise. Also try using fresh hay, if at all possible, in his litter box. Bunnies eat, poop, pee, and relax in their hay box (litter box), so you must make it as enticing as possible! Clicker training probably would not work as well as a nice, fresh hay box in your bunny’s very own, special area!