Nature's miracle works great! I have used it on everything - carpet, tile, wood, furniture, etc. I would test it is a small area just to be safe, and as long as you don't see a difference, go over the woolite areas too, since it could be that there is still a stain there from the urine. Nature's miracle is an enzyme cleaner and if you have a puppy I would go ahead and invest in the gallon jug. It breaks it down so even to the dog the area no longer smells. I've used it on urine, poop and vomit before and we have added it to our carpet cleaner instead of the shampoo if we are out and there is an odor for any reason or to spot clean.
You can also use a 50/50 solution of vinegar and water, but I don't know if that gets everything out as well.