You should keep moms and litters separate from other moms and litters, and from other adult cats. There are several reasons for this, the biggest being territorial behavior among the queens. I have one queen who steals kittens from other queens! It causes fights like you would not believe. Another reason is for the health of the kittens. If you get a sick kitten in one litter (like an upper respiratory infection), you can more easily contain the problem if you've kept everybody separated. Otherwise, you'll soon have every kitten in every litter sick with the same URI.
I have several things I use for isolating litters or cats. A playtent that's supposed to be for human babies, a tent that I normally use at shows but has enough room for mom and her litter, and I use separate rooms, even spare bathrooms, to isolate cats. You can also get a small cage. If you don't have enough spare rooms to do the isolation, let me know and I'll find you some websites or phone numbers to get tents or cages. There is one important thing though if you have to resort to tents or cages. You need to make sure mom gets out every day for a little while. That's why keeping them in separate rooms really is best.