I keep my rodent production in my unfinished basement. I use a custom ventilation system in the ceiling working 24/7 to pull out the ammonia and send it outside. If I lose power even for a few hours the house becomes intolerable (hence the backup generator and spare fans). It was a tough 'sell' to my gf to let me use the basement for my rodents when we moved in...but I convinced her: since the levels of radon in my basement are crazy lethal...and if my professional radon mitigation system malfunctions: the rodents are going to be the first to drop.
Note: I live in a semi-rural area and I keep a water bucket trap outside beneath my ventilation exhaust. I catch at least one wild rat or mouse a day checking out the scent (which over time adds up to a lot of wild rodents drawn in).