White Vinegar is the ultimate in natural dog/cat urine cleaners. Blot up as much urine as you can, then completely soak the area with undiluted white vinegar. Be sure to let it soak in well enough to reach all affected layers, including padding and sub flooring beneath carpets. Blot the area again and allow to dry. This should take care of the smell and remove any stains.
I have also used, and had good results with Natures Miracle and OutRight which can be found at pet stores.
The key to success is use more then you think is needed so ALL affected areas are reached by the product.
Good Luck !!