I like Jules' idea. I think building some sort of pans would be neat. I know that I always have to put shaving on the comfort shelves that come with my mice's Crittertrails because otherwise they would get all pee/poop. YUK!
Whatever you decide, good luck! And with a three story ferret cage I am sure they are very happy rats!
But, yes, I also agree when I suggest not building an enclosed cage. It may contain smell and dropped feces/shavings/etc., but then all that means is all the smell is trapped inside with no ventilation.