Hello! What kind of bedding does your bunny have in his cage?
I would suggest having a cage or pen bottom that is a rug or linoleum. He may not like the bedding, and also by providing a cage bottom of rug or linoleum (you can buy cheap rugs or mats at Big Lots or something like that) the bunny will not confuse his bedding with litter. Also, by having a flooring like that, you can pick up all the poops, and use vinegar to clean up any pee, so that way there will not be any oos or pees left on the his cage floor so he can start to realize thats not where he's supposed to go!
Also, have you put a layer of hay over the litter? That is the only trick I use to litter train bunny - by putting a big layer of hay over their litter, they tend to eat and poop at the same time, and hence are going in the box! You can see some pictures in the habitat section with litterboxes with hay in them, as well as pens with rug or linoleum flooring.
Lastly, bunnies tend to make "territorial poops" in new places, so he may be making some territorial markings, but in my experience that only lasts a few days.
Also, there is some litter box training provided on this page of this website: http://www.binkybunny.com/Default.aspx?tabid=62
Good luck, let us know how it goes!