I have been using a tool my friend Alex Kirk told me about a ways back. It is called "bible arcing". It is a method for studying God's word by diagramming the flow of thought in a passage. I believe it is something John Piper uses having learned it from Dr. Fuller. It has been a huge help for me. Check out one of my arcs below. (I'm still learning.)
Go to http://www.biblearc.com/ for more info. Enjoy!