Hey there - have you worked on litter training him? If he is not going in the litter - it sounds like you need to start from scratch with him and litter train him.
A bunny's pee and poop will smell always - the litter is what will control the odour. If he is not using the litter and you are not able to clean the pee and the poop up right away - you will always have to deal with the smell.
To re-litter train him, you have to have him in a smal area (small pen or cage) and leave him in there, picking up all his poop as soon as he does it and putting it into his litter box. You will also need to wipe up any pee he does outside of the litter with a napkin and put it into the litter box.
After a short time in the smaller pen/cage - he should start to get the idea. When he does, increase the size of the area and do the same thing... slowly keep increase the area he is allowed to play in and he should figure out that he has to pee and poop in the litter box.
My 2 bunnies untrained themselves and I had to retrain them.It tok me a weekend of constant monitoring and having them locked in their cage (and not at all happy about it)... but by the end of the weekend, they were going in their litter box more consistently.
Also - maybe you need to put down more litters than just one if your bunny likes to go in multiple places. I have 3 litter boxes in one bedroom, and my 2 bunnies use all 3 of them.
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Nadia