I don't think you really need to write anything down. The book has the useful and required formulas highlighted very clearly. I have highlighted some parts that are useful for the MCAT such as what is not required and what kind of questions could be asked and in what manner. For me, reading was sufficient enough to take in the information but it could be that I'm that type of a learner. If you think that writing few things down will elevate your level of understanding, than by all means you should. Writing down mnemonics help also.
EK recommends that you do a fast read of each chapter, as if it were a novel. Then go back and reread the chapter, taking notes/highlighting your weak areas, and do the in chapter questions. When you are done this, do the in-class chapter exam.
I read through it multiple times but I also wrote notes on just the stuff I didn't know very well. In the end, I had 10 pages of notes all with really high yield stuff that I didn't know too well (hormones, kidney physio, organic etc). These were very portable that I could read whereever whenever.