Put real (not artificial) vanilla extract in the water to neutralize the smell of their pee. Use rocks in the cages because rats will be more inclined to pee on the rock than their litter. Periodically clean/sanitize or replace rocks. I find that you can easily litter box train rats if you use a sandy substrate in a shallow Tupperware dish in one corner and have some patience to put the stray rat raisins in the box whenever they go elsewhere. They'll get the idea in not very long. Having my males using a litter box and a pee rock has really cut down on the musk.