Cleaning large amounts of cat urine from an occupied house?
I thought they were a gimick at first, but I have had great luck with the "urine destroyer" type enzymatic cleaners.  They promise that their "unique enzyme formula" (unique... they all say that) attacks and breaks down the odor causing elements in the urine.  I haven't taken the time to research their claims, but we have an old dog with a bad bladder, and the stuff works well on her accidents.  It really gets rid of the odor.

My suggestion is to get a quality UV light (careful, cheap flashlight units don't work well) and some good enzymatic cleaner and soak all the current stains.  Once that's done (and you have to let it sit and work until its dry), I'd rent a carpet cleaner and use stain remover to handle any remaining visible stains.