So after about a week Sir Rupert seems to have gotten the message of pooping and peeing only in the litterbox... the trouble is, I have two in his favorite corner currently and he seems to prefer both of them fairly equally, and I don't really want to have to keep cleaning two litterboxes but I can't cover both "areas" with one box.

My question is, should I just pick one and remove it and hope he'll go in the box that's left? Also, I'm thinking of slightly adjusting the shape and location of the pen (only a few inches every which way), would he try to go in his original spot if I move the box a little bit to the new corner, or would he "get" that he's supposed to go in a box anyway?

Rabbits normally go in a corner so even if you move them pen and his litter box was still in the same corner he should get it. You can try taking away the litter box and he may just go in one if all of his hay is in there.

I actually don't put hay in his boxes anymore since he doesn't seem to need the encouragement, and he doesn't poop where he eats either. My vet says it's because rabbits like keeping their food place and their poop place separate -- seems to go against everything I've read about putting hay in or near boxes, but it's worked for me. In that case would he just get that his box moved? Or should I put hay in there anyway just to make sure?

You can just try moving it out and if he still goes there add it back in. I don't think rabbits honestly care where their hay is. They do like to eat AND poop at the same time so that is why people say to put hay in the box. I personally put it in a hay rack above the litter box because my rabbits seem to pee a LOT and I don't like them to eat peed on hay. Its really up to you whether you add hay or not.

What kind of litterbox are you using? Maybe a larger cat litterbox would work well for him? One box, but with a larger area.

I also have my hay in a box suspended over the litterbox. My buns love to eat and poop at the same time, plus ti has the added benefit of keeping the scattered hay confined for easy clean-up.

I have two litterboxes at the moment, one "medium" from BB.com and one small that I got from the shelter, that is arranged in an L shape. He tends to only go in one corner of each box, but the larger one would be unable to cover both spots on each box (i.e. he'll go on the very left top corner of the large box, and then the right top corner of the small box). I also dislike putting his hay there because it's next to the wall and my rack tends to make a mess since it actually hooks on the outside of the cage and Rupert likes to push it sometimes if he's reaching up for hay. Well, I'll try removing one of the boxes and retraining him to use the one this weekend and see how it goes. Thanks for the advice

Blah, update:

So at first when I removed Rupert's smaller box he was really good about going only in the large one. I have a rack on it so I would only dump out his poops a few times a week and not refresh the litter. However I did a full pen overhaul/cleaning this weekend (one to protect the hardwood flooring, two because the alfalfa and hay flakes were getting under the carpet and just everywhere), dumped out the soiled litter, washed his box with water and now he won't use his box!

I have some hay on the floor and some hay in the box, and it seems like he'll only poop on the hay on the floor and not use the box. The only changes I made were the location of the hay (it's between his food bowl and litter box) and the addition of a timothy hay mat. He'll still only poop in that general corner, just not IN the box. I can try to move his hay mat back to where it used to be, but I have a feeling that he'll still just poop in that place regardless.