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When I'm learning new material, it helps me if I take notes (I usually use emacs org-mode). I read on Xournal (annotating on the way) and Alt+Tab to emacs to punch in important points. My question is:

How organized should my notes be while I am authoring them?

The way I see it, I can either make chapters-sections-subsections etc. while I am writing the notes (but this breaks the flow and is sometimes I feel it is irritating since I'm fretting on unnecessary details) or I could write the notes as bullets and organize them later (Something I like but overhead time is spent on organization after reading).

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    I think this is a question only you can answer. Does keeping your notes organized help you organize your thoughts? Are you really going to refer to your notes later, or are you just writing them into your brain? If you refer to them later, does having them organized actually help, or do you benefit from having to reorganize in your head? – JeffE Jul 11 '12 at 19:23
  • @JeffE my question is really about how much I should bother about organisation while I'm writing them. I'll no doubt be organising them sooner or later for my reference. – user107 Jul 11 '12 at 19:26
  • So, what have you tried? – JeffE Jul 11 '12 at 19:29
  • Both actually. If I organise them while, I break flow. If I organise later, I end up wasting longer time and also lot of time wondering "where should this point go?" – user107 Jul 11 '12 at 19:31
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Here's the method I found works best for me:

  1. Read a section
  2. Put the paper down, summarize verbally (mentally or out loud)
  3. If you can't summarize, re-read the section. If you can summarize, write down the summary.

This method has the benefit that your notes don't reflect the stream of consciousness that I found went through my brain as I read the paper, but rather only a concise summary of what I actually understood from the paper.

Note that there were definitely papers where I read a particular section numerous times and had no idea what it was talking about, and I wrote that in my notes (e.g., "The authors then performed a mathematical transform involving technique, and I was not able to figure out how it works from reading the paper.").

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