There's a great item for cleaning car apolstry called "tuff stuff." It will take the stain out of the cushion cover. As for the smell, don't waste your money on Frebreeze. Your couch will just end up smelling like somebody peed on a bunch of flowers until the febreeze wears off then it will just smell like urine again. The product I've found that works the best is call "odorcide." It comes in bottle with a pump spray, costs a lot less than most of the deodorants on the market, and will take the stink out of a turd. I bought a couch one time that had obviously been used by dogs as a bed. I used two whole bottles of Febreeze on it and it still smelled like a dog-like a wet dog that had been rolling in orchids. A friend suggested odorcide. I used it one time and the dog odor was completely gone. I didn't even use half of the bottle of odorcide compared to the two big bottles of Frebreeze. You can pick up both tuff stuff and odorcide at Wal Mart.
Good luck.