Eliezer has recommended that one read them twice. I found this helpful.
Yeah, I really didn't understand the metaethics sequence the first time, but now consider it to be a clear and important section. The difference was in my own ability to understand. I think this is a good reason to do rereading rather than notes or flashcards.
I'm just beginning to go through Rationality: From AI to Zombies. I want to make the most of the lessons contained in the sequences. Usually when I read a book I simply take notes on what seems useful at the time, and a lot of it is forgotten a year later. Any thoughts on how best to internalize the lessons from the sequences?