The first time it is best to study the subject in detail, endeavoring to understand how all the different facets of the subject fit together and interrelate. Then the second time the subject is studied it is a good idea to take notes. The best method of note taking that I know is Mind Mapping, invented by Tony Buzan. You can read about Tony Buzan at this site. His method of Mind Mapping integrates the ability of left and right brain so that you can use the whole brain to understand and recall a subject in its entirety. You can learn about Mind Mapping online here. You may also find his first book helpful - it's called Use Your Head.
I strongly recommend using Mind Maps for note taking, since this method is designed to help you understand how each part of a subject studied relates to each other part, using the right brain's capacity for understanding the relationship between things. This aids memory recall. Once you understand how things relate and work as a whole it is a lot easier to recall the various parts of the subject studied, because they are no longer discreet pieces of information but are understood as an essential part of the "body of knowledge" you are seeking to understand and remember.
Taking notes in Mind Map form, from the second time you study, enables you to study your subject for the third time using the mind map format, instead of, or alongside, the text books. By memorizing the mind maps in the third session of study, you are memorizing the subject in an integrated way. It is this integrated remembering that enables a high degree of recall and understanding.