I don’t cover the bottom of his cage with bedding anymore, i thought it would confuse him during litter training. Which he seems to still need, as he poops/pees where ever he wants still. 
I started putting dish towels in there with him, to make him feel more comfortable leaving his litter box and then also entering his cage after running around. But he would just sit in his poop/pee and wouldn’t even go into his litter box while the towels would be in there.
I’m trying to think of other options, could i put matte tape along the bottom in strips? Would that give him some kind of grip and not hurt his feet? I think he cant get a grip because the hair on his feet is longer than our other bunnies is.
He did have a grass mat in there, a small one from Oxbow i bought while at the vet a while back. He would rarely sit on it, if he did he would pee/pee on it, i’ve noticed that he isn’t a chewer.
Which is worrisome, as he doesn’t chew on wood sticks, toys, or cardboard. He wouldn’t even chew on the grass mat like our other bunnies would. I bought our bonded pair a large one when i got Onyx his small one, and they slept on it for the first week and then began eating it when we had a gap in hay shipments. They are chewers though, Pumpkin is famous for ruining cords.
Onyx is running around in my room right now, i cleaned it up last night as it was pretty messy, and seems to be happy. I set out his morning pellets, and of course he attacked those. I decided to give him Alfalfa again to see if he would eat any hay, and he started munching on it. And set out his water dish, and he immediately started drinking. 
Update: (about five minutes later) I heard tons of sneezing behind me, sneezing and squeaking combined as well. I got up, went over to Onyx to see what was going on and i picked him up. Brought him over to my desk where i could see better (more light) and he was really sensitive about his nose.
So i try to get him to let me look at it, and i was very surprised. He had something stuck in there!
I quickly grabbed some tweezers, cleaned them, and he huffed out a small crumb lookalike. Then he started sneezing again, and with the help of my tweezers, a huge chunk comes out of his nose. I think its time to get him an x-pen until i find out what he sniffed into his nose. 