I agree with Heather....he has to have litter boxes outside of his cage, even if he doesn't get out much. Just remember that you do not get to choose where the litter box is placed, he does! Go to www.rabbit.org to the Behavior link and read up on litter box training. This is a free and very valuable web site for bunny owners.

The other thing is that the hormones in a rabbits body takes 6=8 weeks before they completely are out of their system, so if he was neutered about 2 weeks ago,
1. he can still get a female pregnant
and
2. his hormones are still driving him to mark his territory

You need to stop this bef it becomes a habit. I would try putting a litter box on the floor right next to the corner of the couch he has chosen to "honor".

Also he could be objecting to your brother, seeing him as a competing male......don't laugh, many unneutered male bunnies will claim their female human friend as their mate, so this is not as bizarre as you might think.

Good luck.