You will not get urine smell out of carpet. If you havnt already, you need to use the "crate method" to train him, and/or restrict his running around the house to places wihtout carpet.
Do what you can to soak it up as fast as possible on carpet, soap and water works well, then let it dry.
Try boiling lemons/lemon juice and water and letting it flow throughout the house. Works pretty good.
Febreeze works well. You'll eventually get sorta used to it, but anyone visiting will quickly know u have a pet
No Rinse shampoo weekly or between baths will keep your pooch smelling great and wont harm his skin.
Good Luck.