Yes, one litter box per cat, and being scrupulous about cleaning it (some cats are VERY picky, and won't use a box they deem 'too stinky'), and I do think Moosmom's advice is apt. Once the situation is better under control, he can work on expanding their zone of free reign, and I am glad you haven't just given up on them or made them outside cats when they are obviously inside kitties. I am glad they have been to the vet, so now he can work on the behavioral issue.

Good luck, and let us know how it goes!