It may be a while before the poop ends up in the litter box. You have a few things going against you at this point. He's a baby rabbit, he's in a new home and will be marking his territory for a while, and he's not neutered yet. He may or may not get better at it as he gets older and gets used to being in a new place. But it usually takes getting them neutered when old enough, to really get them to poop in the litter box too. It's pretty good that he's already peeing where he is supposed to though. That can often be a hard thing for a baby to figure out.