I underline stuff I think is important in the chapter while I'm reading through, then I go back and write all that stuff down while reading through again, and checking to make sure the stuff around the underlined portions isnt important. If I find it helps my understanding, I write that too. Then I go to my finished notes, read for full comprehension, and recite them while only glancing at the page to keep track of where I am, then I rewrite them without looking.
Its a long process, but you use EK the physics explanations are concise enough that it doesnt kill all your study time.