You could try saturating it with an enzyme cleaner like Nature's Miracle available at pet stores for about $20 / gallon. Let it dry out and if it still stinks - replace. A black light can direct you to the worst spots, if unknown.
Those stains wont come out. Sorry. If you sand them a bit and add some stain to get closer to the surrounding color it can get close. The smell will depend on how much soaked into the floor underneath. If it still smells ...better get a stick up.
How to get rid of urine smell? Try using Simple Solution which contains enzyme that digests the urine or you could also try baking soda with water solution. Just scrub it into the floor with a fairly stiff brush and left to sit for a few hours.