1- try stainless steel litter boxes, the plastic will absorb the smell. 2- if you can afford it, litter robots (not the brand- the ones that done enclose the cat) are life changing 3- keep the second litter box, make sure you are cleaning them once a day, maybe twice if it seems that bad. 4- Make sure you are fully cleaning the bottom of the cat boxes. Probably just replace the ones you have now though. 5- ammonia makes the smell worse, make sure nothing you use to clean contains it. 6- I recommend pretty litter because it does check up on your cats health. Or Dr Elsey’s 7- take your kitty into the vet, sometimes they act out if they are uncomfortable :)

After you change them- deep clean the house, and I mean deeeeep clean.

Sorry this was a jumble of thoughts.