It could be a couple of things; some cats prefer to have a different litter box for pooping and peeing, some prefer to have a different one from other cats. Like Jen said, you need to have one per cat plus one extra. Cats are also very finicky on how clean the boxes are, you may try emptying them completely, scrubbing and disinfecting and adding fresh litter to see if that helps.
It could also be a paw problem, where it hurts to stand in the litter and you should check her paws. You could also try a different type of litter, it may be that she has decided that she does not like that kind of litter.
It could also, like Jen said, be spraying and not peeing on things, and the only way to really check that is to get her checked out by a vet. In the mean time, you should get a strong (but animal safe) cleaner and de-scent those areas. Once they use them to pee and have their scent on them they are more likely to go back there and use the same spot.
It could also be a medical problem that has put them off using the box, as said above, a Urinary Tract Infection (UTI) or if she has not been spayed yet, something to do with that.