You know ammonia when you smell it, and if you can smell it you need to get rid of it. Ammonia's a gas that needs moisture, nitrogen, and alkalinity (vs acidity) to form. It's a problem in chicken houses, but also in the brooder for us pastured poultry growers. The nitrogen comes from excess manure that doesn't have enough carbon (from bedding) to suck it up, the moisture is usually from leaky waterers or in the humid summers, from high humidity, and the alkalinity comes from the excess calcium found in the poultry ration, whether chick-starter, grower, or laying rations. The chickens can't digest all the nutrients, and the lions share goes out the back onto the litter.
One advantage with ammonia is that every person has a built in set of sensors - the eyes and the nose. Most folks start experiencing irritation around 25-30 ppm. OSHA's getting the working limit to around 25 ppm as well, so if the ammonia's burning your eyes, throat, or lungs, then you need to do something about it. The effects are typically short term, and only do real damage after chronic exposure. If you've ever walked into a chicken house with a fieldman or CAFO farmer, the ammonia can feel like tear gas, but it won't even phase them. The olfactory sensors in their noses have literally been burned out. As you might expect, chickens don't like ammonia either, and there's been studies that show that around 15-20 ppm, chronic exposure starts decreasing the productivity of layers and the gain on meat birds.
Most ammonia spikes are due to leaky waterers, and that's our case. This year, we've pretty much stopped any moisture problems and ammonia problems by just putting a board underneath that catches any spill. A thin layer of shavings on top catches any manure, but allows it to dry out a little before I stir the damp, poopy shavings back into the surrounding dry litter. One of our big problems in the past has been letting the waterers run out as well, which creates a sloppy rush of thirsty chicks that spills water all over the place. Better husbandry leads to better husbandry I guess.
Temperature helps drive ammonia formation as well, so there's a positive for winter brooding of chicks - temps too cold to really get ammonia fired up. If you do find yourself with an ammonia problem, add lots of dry bedding and ventilate from the highest spot you can, as ammonia is slightly lighter than air and rises.