IMO if the problem is in the carpet pile and not the backing (like the doc said) DONT USE prochem products! They are so not powerful enough.
Use UCT from ChemSpec (Urine Contamination Treatment) on areas that you now are contaminated with pee, and use Kill Odour Plus to spray the rest of the room.
As for staining, use very hot Spray and Go (basicly sod met), again from ChemSpec then rinse. Cat pee is the hardest of the pee's to get out i find...
Tony