Have you tried Nature's Miracle? Everyone that has recommended it to us SWEARS by it -- the vet, the pet store, fellow dog owners!
It gets rid of pee and poop odors and also eliminates the scent so puppy won't go in the same spot. You can use it on hardwood floors and carpet. If you're using it on carpets/rugs, test it first and if using on hardwood floors, spray it on and wipe it off right away b/c the floor will absorb it if you let it sit.
It comes in spray and larger bottles and it doesn't stink!
(I first heard about it through friends that own a Newfoundland -- he had lots of accidents on their carpet and you could never smell a thing when you went to their house!)
Good luck and keep us posted!
Mojito & Irmi