I have a small rat colony with 2 Males 12 Females and 10-25 babies at any given time and I keep them in the closet of my apartment and have very little odor. I keep them in the medium cement mixing tubs ( 27" x 20" x 6" ) on kiln dried pin. I have two racks - 1 rack with 4 med. cement tubs for breeding the other rack is a birthing rack with 5 large cat litter pans for the females to give birth in and raise their pups.
Add vanilla extract to the water ( was told it cuts down urine smell ) I've done it from the start so I'm not sure how much of a difference it makes.
I change bedding every 4 days and keep 1.3 ratio.
I have a couple of the baking soda odor things you keep in the fridge by each rack
And I have a timed spray unit that sprays clean linen smell every 36min, like the ones in the bathroom( bought mine from target for $10 )
I do notice when I receive new female breeders they smell more than my current rats. I feed different food then the breeder I get them from, I think what you feed them makes a difference in their odor also. I feed Native Earth 18% Protein 4018 Rodent Diet from Pet360.com 40lbs for $26 free shipping !! I also feed a seed,pasta,oats,multi grain cereal and veggie mix once a week. After the new rats have been with me for about a week they loose the stench from the breeder.