One thing for sure, there's no consensus. It's got to be what works for you, and the approach you've set out sounds pretty reasonable.
FWIW my experience is that any kind of detailed notetaking is a waste of time. Most courses have reasonable manuals which serve as a good reference. Sometimes constructing a
table helps structure the info, but really only you know what works for you.
There are some subjects (airlaw, ops procs) where IMHO it's a complete waste of time trying to learn the material in the syllabus - there's just too much. Better to breeze through the material trying to pick up some overall ideas, then bash some mock papers or hit an online question bank. That will narrow the focus on what is examined - otherwise you'll go mad.
Allegedly, the creation of the airlaw central question bank was delegated by the JAA to some portuguese air traffic controllers, so that may help explain why intuition and diligent learning may not be the best approach !
Good luck.