I've only challenged them, so I can't speak too much to how you manage organizing the course materials. Although, I know many people tab the pages. I've posted my recent GWAPT experience here: https://www.infosiege.net/2012/04/gwapt-challenge-review/ if that helps you at all.

To answer your question more directly, I make custom notes of any item on the practice test that I'm not familiar with, and I print out the help output/man pages for all tools referenced anywhere (practice exams, course pages, etc.).

I bring in outside resources (i.e. WAHHv2) since I'm challenging the exams, but you shouldn't need anything else since the questions are all written from the course materials. However, making your own cheat-sheets of things like common tool switches may help you find the answers faster.

Personally, I think you should study to the point where you can pass the exam without referencing the materials at all. You should only be looking information to respond to an obscure question or to verify a fluke fact you can't recall. If you're relying on the materials to pass the exam, you simply haven't prepared enough in advance. If you spend enough time using the tools and applying the techniques, the exam will be a breeze.

Some books have a table of contents, but for the ones that don't I make one first and foremost. Then, I go back and read the books page by page marking where I don't feel 100% comfortable with the material, but the first read through is not for taking detailed notes. Once I've gone through them all, I go back and re-read. This time I'm not re-reading for retention of material except where I've marked during the first read through. Instead, I gloss through the materials and I take notes of what I want to include in the index. A good rule of thumb I use is have at least one entry for every page. Some pages, though, will obviously have more and some won't have any, but I try to find one. My entries for my index are "<term> <tab> 1.11." The first number is the book number and the second number is the page number. Once I've gone through all the books, I type the index up and print it out double-sided, multi-columned.

As dynamik/ajohnson pointed out, if you're looking up all the answers go back to the material and study some more. While they may give you enough time to look up all the answers with a good, detailed index, you're not doing yourself any favors by having to look them all up. I find, though, after going through the class and reading the books multiple times, I usually know the material fairly well.

My GSEC instructor gave some good advice, I think.  He said to first, read all the books again.  Then take the first practice exam without using any books or prepared notes.  Take note of the questions you have problems with, then create an index of the topics (topic, book #, page).  While creating the index, study what you had problems with.  Then take the 2nd practice exam using the index/books when needed, taking note of questions you have issues with on this exam.  Go back, update your index while studying the topic.  Then you can go into the actual exam with your books and an index of problems areas, just in case you need them (nerves get the best of you, etc).

I just took my 2nd practice exam for GSEC, improved my score by 9% and barely used the books.  Studying the topics while creating the index really helps

This is really close to what I did for my GCFA. The first practice test was great for showing what what material to prepare for the test. I improved about the same % on practice test 2.

I read through and tabbed every book I took in with me and had a folder of cheat sheets that I printed out. The four hours flew by and I was rushing on the last part so if I hadn't prepared the way I did I would have been in some serious trouble.