How old is this kitty? Is he fixed yet? Has he seen the vet?
It's possible he doesn't like the cover. Some kitties are very particular about their boxes and won't use them unless they are very, very clean. It would be good to have his vet rule out any health problems. Neutering as soon as is age appropriate should prevent any marking issues.
Also, be very thorough in cleaning it. I would get a really good cleaner like
Nature's Miracle or something similar and follow the manufacturer's directions to the letter. This may even include pulling back the carpet and saturating the carpet pad with it. If kitty can smell where he's been, he'll keep using that spot. Also, you might want to buy a cheap hand held blacklight if you have carpeting so you can see everywhere he may have had accidents.