Bunnies typically like to munch and poop at the same time. I use very big litter boxes (rubbermaid bin), fill the bottom with pine pellets and add a huge handful of hay at one end once a day. My guys love to munch, dig, rearrange and yes, poop on the hay (mostly in one corner though). Because the litter box is so big I end up changing it once or twice a week and just keep adding lots of fresh hay daily. The bottom stays lined with the pine pellets and the hay adds a new layer everyday. I also had tried everything to keep them potty trained and keep the hay "contained". I've had my bunnies for a few years now and this is by far what I found works best.