I attach a link to a copy of my research template, a version of which I use for my (sadly neglected) history degree, and a version of which I use in my day job too:
http://cl.ly/3o0t3h2u3s3C1I3t3n46It is heavily based upon this system:
http://calnewport.com/blog/2007/10/01/monday-master-class-how-to-build-a-paper-r...It has 4 note types: printed sources, quotes, lectures and interviews. The way I have used it is to list out all the sources on a given topic (starting by copying-in the course reading list, and adding others as I go) and then work my way through them one by one, building a list of quotes to use when it comes to writing up that dreaded essay or thesis. The quotes are linked back to the Source using a link type called 'quote'.
I have found when taking notes say on a journal entry or a book chapter, I prefer to capture them in a single container rather than starting the whole process in a map view or outline view with lots of little notes. This might not be best practice, but I don't want to think about structure at all when I'm taking notes, I just want to get the words down - you can explode the note later if you want to.
I do take lots of notes when I read, but I agree with the linked article - the key stuff is the quotes from primary sources, and this system is really designed to capture them methodically and reliably.
The huge advantage of Tinderbox over other systems is that once the information is there, it can be analysed in so many different ways. I use agents to search for themes. You can also open the various note containers in map view and play around with grouping things into themes. Try smart adornments for this. As I am interested in history, I make good use of timeline view. One of the best ways to identify themes I have found is to use Common Words in the View menu. Click on a word and you run a search. In the attached example, the quotes bucket only has two quotes but no doubt yours will run to thousands. Initially, I would start by using seperators to mark off divisions of notes in the outline, but once past hundreds of notes this would get difficult - at which point, agents would be very helpful to captures notes by theme.
Tinderbox is great for tracking what I've read, linking quotes to notes etc. But I use lots of other programmes too and then link to them in Tinderbox (I think it really helps not to be too rigid when doing this stuff - you can agonise over which programmes are best for certain 'workflows', but I think its best just to get on and read and write, and then sort the notes out later in Tinderbox).
Edit: On a related note, ages ago someone here posted a link to a chapter of
The Social Imagination, by C Wright Mills, in which he explained his method of note taking. I thought it was quite interesting and did a little summary of it (far too simplistic for the OP to find of use):
http://cl.ly/3q0I0L0p1e0o223n2J0BThere are two really simple points, with which I agree: 1) in order to understand something, you must give form to it and 2) avoid any rigid set of procedures, method or technique.
Ben