Well, as much as anyone can ever explain it, I guess.
But I do recommend these two readings from the Writing Center at Boise State that I came across while looking for something else. They take a sensible approach to the topic while navigating between the "rules" method and the "throw it in wherever you think it's needed" method.
Punctuation as a system, the hierarchy of punctuation: http://www.boisestate.edu/wcenter/ww81punc.htm
Focus on the comma (with an excellent section on why the "pause" method does not work well): http://www.boisestate.edu/wcenter/ww109.htm