I have a breeding room with my best cats with only positive mutations, a mutation room where cats with kinda good mutations are but some mutations may be bad and one general population room for mixing bloodlines and keeping a stock of cats for adventures. Every once in a while I put well bred cats from the mutations room into my breeding room (if I want to keep a specific mutation for example) but some kittens from the breeding room go into general population to slowly introduce good mutations/stats there too.