I rescue kittens and have trained a few from birth as there was no mom to do it. I believe a small area is good and i have around 10 boxes all over and different litters/ sizes/ lids but I am a real crazy cat lady
I also have a huge (5000sf) home and cat doors into our contained fenced yard. My vet has always been great to help me with difficult issues. I bet once yours feel better, the problem will be solved. Good Luck!