Bunnies love to munch while they go.
So, if you put hay in the litter box, they will like going in. Then start expanding their space slowly. They will start considering those areas theirs and they will tend to keep them clean. Positive reinforcement - pets and nice words will also encourage good litter habits. You can also use bathmats, which are easy to wash and have a rubber backing to prevent pee from getting on the carpet or floor.