It takes time and patience. In the early stages of training place several boxes around the area the rabbit runs. As the rabbit catches on, remove the boxes one by one so that only a few remain. Rabbits learn much easier as they get older. Be careful what type of litter you use.
Rabbits are different than cats in that they tend to ingest some of the litter.
Clay litter is dusty and can cause pneumonia. Clumping litter is ingested and clumps in the digestive track. Corncob litter can also be ingested and can cause a lethal blockage. Paper pulp litters work pretty good. Litters made from Aspen bark work well.