Does anyone know if there exist a Latex manual with focuses on chemistry and perhaps also system biology?
I suggest follow the tohecz's comment. In www.ctan.org/keyword/physics there are a easy index of packages associated with the keywords of Chemistry, Biology (and Physics, obviously). Browsing in the directory of each package usually you can find a pdf manual (probably also in your hard disk).
May be is also worth to mention the article LaTeX Tools for Life Scientists (BioTEXniques?).