What sort of gravel do you have? Could it just be fine sand, silt. Its not ammonia- you cant see that. Fish waste is the colour of your fish food. Dont stir your gravel up so much. Do you have a gravel cleaner? Just work your way around the tank plunging it into the gravel and giving it a little wiggle ull see the waste free up and get siphoned out.
Fully cleaning your gravel (thus giving your good bacteria a hard time) could have killed your cat fish with the subsequent ammonia spike as you have upset the balance in your tank by killing your bacteria. A test kit would help monitor ammonia, nitrites after you have given it a good clean. A nitrate test would be handy if you dont feel like cleaning your tank but want to check if you have too much waste in there.
Easiest way is to stay on top of the maintenance, depending on your bio load, every 2-3 weeksish.