All my litterboxes are covered and I have a air purifier with an ionizer on it. I use Feline Pine and it works really well.

Sounds like your cats might not be drinking enough water. A concentrated ammonia smell is usually an indication of that.

I have 8 cats. I keep a PetMate Water Fountain going all the time and I also have 3 bowls of filtered water that I change at each feeding time.

I really have no suggestions except to maybe get them a water fountain (my cats LOVE it and it's paid for itself already!!) and covered litterboxes.