I found two great things to help with smell. I use pee pads under the hidies and the food area so that I can wash those more often. I use them for two days, spraying them with Cage Clean and then flipping after one and then washing after the second.
I also only use ONE layer of uhaul pads underneath. I find that the pee dries very fast that way and that gets rid of the smell faster because it is drying and not staying wet under there.
As for marking, find a place that the boar marks, maybe put TONS of pee pads down for a few days, and then leave one marked piece of fleece in the cage. It will still smell just a bit, but it will keep him from marking further. My boys have their "baby" (a smelly bit of fleece) in the corner by their hay, hanging on the wall. It seemed to cure the marking while in the cage. They still mark my whole house when they are out, but whatever.
Cage Clean is a great deodorizer. I spray it on the pee pads daily (and then turn them sprayed-side down so the pigs don't get that smell in their face). It helps lots.
I'm also considering getting a small air purifier to go next to the cage. I've heard (I think from bpatters) that it really helps.