Glad I ran across this thread. I have a similar problem. There is one room in the house Charlie has done a good job at "marking". You can smell it.
It got real bad when they were building a fence in the backyard and I wasn't able to let him out back as freely.... Well now he's doing great going outside again, but the urine smell is still in that area. I put some arm & hamor pet spray stuff on it but it seemed to make it worse. I was considering renting a steam cleaner from home depot, but looks like some of you haven't had luck with that. I'll have to check out that bot spot stuff before cleaning the carpet.