Here's some more info for you: Putting hay in the litter box also helps because they like to munch on it while they go.
"Litter Box Training
The most important thing you can do to improve your rabbit's litter box habits is to have him neutered or her spayed. Most altered rabbits will train themselves within a few days if you simply put a box in their cage and then place it or another box in a favorite corner every time you let your rabbit out to play. They are creatures of habit and will always return to the same place to "go". We recommend filling the litter box with newspaper, a layer of nontoxic litter (optional) and a large top layer of fresh hay. The hay will attract bunny to the litter box. This is not unsanitary, but rather a natural way for your rabbit to meet all his digestive needs efficiently! Just make sure there's always fresh hay on top: they usually use only one corner as their bathroom. Regular clay cat litters are not good for rabbits as they are too dusty. Never use a clumping litter as they can be fatal. Even though most pet stores sell them, cedar and pine shavings should be avoided as they cause liver and kidney damage. Safe litters for your rabbit include the recycled newspaper ones such as Yesterdays News or Carefresh. Another good choice is wood stove pellets that you can get at a hardware store such as Home Depot. Newspaper is the cheapest option but requires daily changing.
It is very important to spay or neuter your rabbit. Most importantly, it prevents unwanted litters and helps with the overpopulation problem. It also provides health benefits including prevention of reproductive system cancers which can strike both male and female rabbits. Also, both male and female rabbits can spray and exhibit sexually aggressive behavior unless they are altered. These behaviors include excessive digging, marking territory with urine or droppings, nipping, fighting with other rabbits, and "humping" everything within sight. Once your rabbit has been "fixed", the hormones and instincts which cause these behaviors are reduced and your rabbit will be happier, more relaxed, and more enjoyable to have around the house!"