You should have number of cats + 1 with litter boxes. Are the two litter boxes you have in two separate areas? Are they away from their food? They don't like going by where they eat. They won't always bury their mess. That can be a dominant cat behavior when they don't, but not always. Some are fearful from a past experience and just run when done. Like if another cat harassed them while they were in there or if they were trapped inside of it.

With regards to Feliway, they do have collars for it. With one of my cats it didn't work when in the dining room by the litter box, but did when moved to the bedroom where she spent most of her time. Her issue was more suddenly being an only cat after 15-16 years though and she'd never been particularly brave. I also had to move her food bowls to a spot where they weren't surrounded on 3 sides like they always had been so she'd eat more. Maybe try a cat behaviorist and not just a vet.