My best advice is to neuter asap. I picked up a rescue from a pet store, so I am not sure how old he was. He was still quite young but old enough to neuter. He went straight from the pet store to the vet. He has perfect litter habits, naturally (meaning I didn't do anything special to train him.)
For contrast, my older bunny wasn't neutered until he was years old. Because of him, I still have to vacuum and sweep every single day.
I can tell whose is whose because the older bunny is a 2 pound dwarf and the younger bunny is pushing 12 pounds.
The next advice I can give is that they like to poop while they eat, so place their food in such a way that they have to sit in litter while they eat.
Hth.