This guide provides an effective approach to organize notes. It's also as an example of how to apply the technique.
Cue points here
Explain points here
Take notes here
Record thoughts here
Summary is optional.
Seeking the Productive Life: Some Details of My Personal Infrastructure-Stephen Wolfram Blog
Wolfram shows how he organize his notes. Isn't that an art?
A friendly HOW-TO guide on organizing notes.
Feeling Scattered? How to Organize Notes to Stay on Top of Things
Author's strategy: take a pause, stop everything, and then get a page of notes; sort it out, put each one in its proper place; pick up another and put it where it fits, and so forth.