Still working on developing a system of notetaking that will work for me.
Here's where I am now.
While doing background research for a book, I find it necessary to read several dozen books, magazines, reports, and other documents. Facts taken from these documents must be summarized to I can use them in my draft, and 'sourced' so I can go back to the original document later, if I need to verify a fact.
I have a terrible memory, so I have to devise a systematic way of keeping track of what I read, and where I read it.
Before starting notetaking, I enter the book title in RefWorks, so I can generate a bibliography later.
1. Read and annotate the book.
2. Go through the book with a stack of 3 x 5 notecards.
Write concise notes describing the annotations on the 3 x 5 cards. Write concise summaries in your own words, do not copy, do not write prose. In the upper right-hand corner of the card, note the source -- book and page number. Work quickly.
3. Sort the cards into Chapter piles.
4. Sort Chapter piles into section piles.
5. Stick the cards on a display board.
Rearrange the cards until they feel right.
6. Referring to the display board, write the first draft.
7. Insert bibliographic citations as I write the draft, using the RefWorks Write-N-Cite utility.
In this approach, books are consumables. Much like film stock in a film production, the books are consumed during the project.
I hate to write in, or highlight, books! I'll spend $500 going to a seminar as part of background research, and never blink an eye. But writing in the margins of a $5 book makes my skin crawl.