If you want to find the worst spots in the carpet, buy a black light. They sell them at Petsmart and Petco. Theoretically, the less evidence of himself your puppy smells the less likely he is to eliminate inside.
My puppy had a bladder infection a couple of months ago. After he was better, there were still some spots in the house that peaked his attention. One black light and one steam vac (and one neutering
) later, we've got a perfect little puppy.