From reading others experience and from mine with Willow I’d say each bunny is different and can be very particular about what suits them. Assuming he’s neutered, i think if you found something that works, definately stick with it.
Willow is particular about where her boxes are, and though I would prefer not to have one in my kitchen, it’s her favorite place to go so there is a box there. WE have to change that one daily now and it almost needs more than that since she uses it almost exclusively and its a small one unfortunetly. I’m afraid to change it to a different style since she may not like it.
Her only problem area was our bed. We kept her off it for about 2 weeks and still only allow access if we are there and knock on wood it seems to of stopped that behavior. I think I’d keep yours off the carpet till his consistently going in his boxes. Hopefully that will get him to get some good habits, and perhaps break the habit of the carpet. It can give you some time to hopefully get any smell out of it that he will notice as well.
As far as softness in the litter box, if newspaper works I’d probably stick with it. Do you use hay in it? I know Willow likes the hay spread over the wood pellets, I’m sure for the softness as well. The hay is cheap since we get bales and I’m sure I’d have to toss it for being old before she’ll ever get through the whole thing. For cheap paper you might ask neighbors, friends and family who get the newspaper to keep them for you.