I’m quickly going to run through how I use scrivener. Unfortunately I am dead broke, otherwise my workflow would be including Mellel/Bookends. As it is I’m gonna see if I can get BibDesk to work nicely with Word 
I don’t own Devonthink, and to be honest I use del.icio.us to organise my online resources.
My personal situation is a Postgrad Masters course, but it is somewhat ‘taught’ and my techniques could easily be used by undergraduates. If I could I would be taking my class notes with the laptop, but these are small classes and it would be extremely rude and intrusive to do so.
Anyway, here is my main method for class stuff over a 15 week period, based somewhat on GTD, and also on using a little repetition so I have the concepts from class down correctly before I just start writing/thinking critically.
Scope: Take down notes and useful info in a clear and organised manner, enter info so I can find it later, and also absorb info by re-writing and organising it.
- New Project Binder
- Labels: Initial Lectures Notes, Secondary Notes, Assignments, Follow-ups, Big Questions, Snippets/Quotes
- Status: To Do, Rough, First Draft, Essay Ready Concept, Done
- Keywords: I write these down during class - names that come up in class, jargon, broader themes etc. I start off with an initial set by some preparatory reading before the introductory class.
Folder Structure
One Top Level Page with information about the course - Tutor name and contact details/office hours, what work is expected, where the room is, the class code, the examination system, due dates etc etc.
Scope: Because I have a 2 hour seminar each week for 15 weeks, I create a folder for each seminar labelled Week #.
Each folder looks like this
- To Do for this Week
- Initial Lecture Notes
— Subnotes/Elaborations on individual points within the lecture. - Assignment From This week
– Answers/Notes related to this Assignment
This results in some dupelication, e.g. ‘Assignments’ from week one should also be linked somewhere in a to do file in week 2. Scrivener’s internal linking is great for things like this, as you can dump clippings and things in the research folder and then link it from anywhere.
Use keywords without, so you can track themes through out the course (e.g. I am studyingWilliam James – one of my keywords is Dewey, which tracks all references/stuff related to the social scientist in the context of James.) Use the status and labels to keep track of specific types of notes (e.g. lists of questions to ask, further research to cover) and status to…well, get a quick oversight of what you still need to do.
You should also create one last top level folder specifically for work which you will get graded on, such as a major presentation or paper to be handed in at the end of the term. A great keyword is ‘paper topic’ or something similar - use that to gather together those possibilities.
I would make a separate binder/project for the paper itself, but it is good to have it in the same folder as your lecture notes.
I’m actually going back an transcribing my old notes. I wish I had done this sooner, as my handwritten notes are horrible!
Hope someone finds this useful.