Bedding mistakes for new hamster

[Marshmellow]

Hi,
I am new owner to 2 Syrian hamsters(they have separate cages). I have owned then for about a week. I didnt fully research bedding and am pretty sure there is not enough bedding in one of the cages its only a couple inches deep. I had planned to just add more bedding but his cage smells terrible. He took to.peeing everywhere the first couple days. Now he has one corner he uses with sand in a litter box but Im not sure how to handle the order. DonInthrow more bedding on top of the soiled bedding? I dont want to stress him out but not sure how healthy it is for him to be in a cage with the smell of ammonia all over most the bedding. The corner his nest is in is the only spot that doesnt smell! Help. I considered dumping most ofnthe bedding from the areas other than his nest and not disturbing it and leaving the litter box alone as well but is that too stressful? Id love some advice on how to handle this situation. Other than this he is happy healthy and very friendly.