Im not sure about the chemical byproduct. But i bet someone will chime in and fill us in. I would have to say the best way to get ideas for setting up a new tank is to check out the
http://www.talkingreef.com/forums/member-tank-projects/. You can get alot of good ideas. Thats were i got most of mine anyways.
Also if i had to make a suggestion about starting a new is get a good
skimmer and light. Almost everyone i know replaces the original light and
skimmer within the first year or so

Happy Reefing