Karen has given you great advice. Young bunnies require a lot of patience.

Putting timothy hay in the litter box is a great incentive for the bunny to learn what that box is for.

Young rabbits are generally more difficult to litter train only because they are very energetic and busy exploring their world and, like a small child, don't want to take the time out to go use a toilet(litter pan in this case). As they get older they do become more discerning about their living environment and most buns will begin to only go in one or two places in order to keep their habitat clean. There are a couple of other great side benefits to neutering your bunny.....his urine will be less odorous, he will calm down and more likely become more affectionate to you. If you think he is lonely, try getting him a small stuffed animal that is the same size as he is.

Good luck and let us know how you and he are doing!