You should place a litter box in the corner of their cage and then
when your bunny is comfortable in his/her cage, you can let him/her out for some exploring. Let him/her out in a small area increasing slowly. By using small areas, it reduces the chance that the bunny will find another spot to use as his/her bathroom outside of what you have in mind. As you enlarge the area, your bunny will choose places for his/her litter box. Set a litter box where ever your bunny decides to "GO". As time goes on your bunny will use the spot more often. Keep your bunny off the bed and furniture until he has strong litter habits. Carrying your bunny right to the litter box after opening his cage can also help teach them where to mark.
 

What Type of Litter is Safe for Rabbits?
Be sure to use ORGANIC litter in the box.
Organic litters include those made from recycled paper products
(e.g. Care fresh, Nature Fresh), pelleted wood sawdust
(e.g. Feline Pine, Aspen pellets) or other pelleted organic products.
Do NOT use cedar
Clay litters--especially clumping litters--are inexpensive, but very unhealthy for few reasons. One reason is they can inhale clay dust that can cause respiratory problems.
Once your bunny is reliable about using the litter box in his area, you can gradually increase his freedom.
 

While your bunny is out and about, it is fun for him to find chew treats and toys placed around his play area. Keeping his mind occupied will help in his/her adjustment to his new home. If your bunny is having trouble becoming litter box trained, his play area might be too big too soon. Also, putting some hay in a corner of his box can help him use it more reliably. A small size cat box with lots of hay in it can act as a great litter box. It should be deep so the hay doesn't get spread all over the floor. It often helps to put a handful of timothy hay in a clean corner of the litter box to encourage use of the box. A rabbit will often sit in the box, happily munching at one end, while the processed product comes out the other end. This may seem a bit strange to humans, but rabbits don't consider their feces to be dirty.
Don’t forget to change the litter box often.