Mr. Fishhead,
This thread is getting long so we might want to start a new one but how far do you get before it gets confusing. You probably do not really need to know how the chemical reactions occur etc. but rather fish produce ammonia in the urine. Ammonia is bad and will kill fish (no one no thing wants to stay in urine  . There are bacteria that convert the ammonia to nitrites and other bacteria that convert nitrates. If you get a test kit you can see the levels of these. When you first set up a tank the bacteria is not sufficient to convert ammonia to nitrite. It takes a little while with ammonia (the food for this type bacteria) for it to grow and get big enough to convert it. Same thing holds with the nitrite to nitrate conversion as well - it needs nitrites available to grow the proper bacteria. If you test the water in a new tank you can watch the ammonia level come up and then decline (in most cases). Then a little later the nitrites will come up and decline as well. Lastly you see the nitrates raise and maybe decline (and water changes help them a lot too). Does this help explain it at all. 
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Loman
24 Gallon Saltwater Aquapod
1 Royal Gramma
1 Blue Devil
1 Bicolor Chromis Lyretail
1 Scooter Blenny
1 Chocolate Chip Star Fish
Crabs and Snails
20 Gallon Freshwater
Swords, Zebra Danio, Neon Tetras, Albino Cat Fish, Plecostomus, snails
10 Gallon QT Saltwater
10 Gallon QT Freshwater (Divided) | 
