Ammonia (NH3) is a cleaner. It's used to clean because it doesn't reduce colors on many objects as bleach will. Chlorine Bleach (NaClO) is better if you are trying to eliminate bacteria (disinfect.) Ammonia's kill rate on molds is good, but on bacteria is quite poor. The great thing about bleach is that it can easily be removed with doses of dechlorinator.
Also, never mix the two together as the combination can release toxic vapors.
Great info here thank you. What about my driftwood/ petrified wood? If old disease can hide in my filter, Im guessing it can be in my driftwood too. How often do you guys disinfect?