Nitrates are mostly used to judge how much water to change how often. If you have reasonable stocking levels of fish, you can just change 20 to 30% of the water each week and toss the nitrate kit. The ammonia/ammonium kits are the ones to tell you whether or not the filter has been cycled and the nitrite tells you about an intermediate process poison that can also harm the fish. The difference between ammonia and ammonium is not important when you are cycling a tank. What happens is that as pH changes, the balance between ammonia and ammonium shifts. Both are associated with the same NH4 ion but ammonium as ammonium hydroxide, the stuff we add for cycling, has a fairly high pH because it is combined with the water molecule, not just dissolved in the water. The NH3 gas dissolved in the water can switch back and forth with ammonium as the pH varies. Both are dangerous to fish and we usually ignore the fact that they are not truly the same chemical. Instead we say things like ammonia being more dangerous to the fish as the pH goes higher and being less a problem for the fish as the pH goes lower. The 0.25 ppm numbers we use on here are really numbers associated with a danger at high pH values. At much lower pH values, the fish a relatively safe with higher ammonia readings because of the form the chemical takes on at lower pH values. Unfortuantely the low pH is only safer for ammonia. When it comes to nitrites, the low pH makes nitrites far more dangerous and the high pH is less dangerous for nitrites. One of the many reasons we don't mess with the pH is because you are not just changing the pH, you are changing which poisons are more likely to harm the fish if they are present.
