Assuming that the reading is for content knowledge rather than process knowledge (that is, it’s about the subject matter and not about how to do something), I use underlining and highlighting, but very selectively. If you look at a page that’s solid highlighter, it’s as good as not marking anything.
I try to organize things in my head as I go along, being aware of the outline that the author probably followed. This is why teachers sometimes make you outline chapters. In order to write the chapter or article, the author had an outline listing key points and subpoints and examples. If you can back it out and derive the same outline from your reading, you’ve got what they were talking about.
So I highlight ideas that seem like the main points. I underline sentences and phrases that strike me as really communicating something useful or new—something that moves my understanding forward. I don’t underline entire explanations—just enough to (a) allow me to find it again and (b) make it jump out at me when I’m reviewing.
In the margins I draw a little square window when i see a good example or illustration that helps me understand. I draw a little light bulb for anything that makes a light go on in my head—a bright idea. I write definitions of words if I had to look them up. And—this might be the best thing—I cross-reference by page number (in both places) passages that tie together with other passages—that connect in some strong way that helps it all make sense.
I also pay a lot of attention to what the instructor says in class. If you listen carefully and take good notes, you will find out what the instructor thinks is important to get out of your reading. I make sure I get that.
Now, if what I’m reading is not subject matter to be learned, but rather things like novels, plays, and essays, like for a literature course, that’s different, and I would not use the same techniques.