Irregardless of the urine smell throughout the house, cats are naturally clean creatures and abhor peeing in an area where they can't cover their urine and feces. When a female is not using the box, it doesn't mean she doesn't get it, it means she's physically uncomfortable. I encourage you to have her checked by the vet- a small price to pay as kidney and bladder problems can be deadly. The problem with cats sometimes is there is only one symptom or none- often they are diagnosed too late to treat because they don't complain- females with uri's don't cry like males (my experience anyway) so it is easy to pay no mind and just figure the cat is having a behavior problem! Call the vet!