1. Your notation should be a way for you to keep track of the thread of an argument. So on one level, you should be underlining and putting notes in the margin that help YOU keep a handle on the argument. Ideally, you want to do this in a way so that when you return to the book, you can quickly reorient yourself to the argument and the main moves of the text. This requires watching especially for transitions and turning points in the argument. (I use the top of the page to note themes I’ll want to find quickly when I page through later.)
2. You need to develop your own way of noting gradations of emphasis. This might be a simple as single underlining and double underlining. Or could be different colored pens, or ink vs highlighter. Whatever. I just find it helpful to have some layers. (This is especially important when you return to read a text again and again—look for ways to distinguish annotations in later readings—you might have to buy purple and green pens! And sometimes you’ll find you need to later scratch out juvenalia. My copy of Of Grammatology is filled with this because I first read it as an ardent undergrad who was clueless.)
3. Use numbers in the margin to track different parts of an argument as it unfolds.
4. Write marginal comments to try to encapsulate key points in your own language. If you’re reading a translation, at some points you might want to note key terms in the original language.
5. Put circled question marks in the margin where you just can’t figure out some point. Don’t get bogged down there, however. Note it, mush on, and it might become clear later.
6. Cross-reference. You know how some Bibles have those elaborate cross-reference systems? Do something like that yourself: point back and forth with marginal notations like: “Cp. p. 17” and then go back to 17 and note the other page.
7. Argue with the author in the margins. Put big Xs (or “B.S.”!) beside passages that deserve critique. Perhaps briefly note your critical point.
8. Finally, and maybe most importantly treat the hors-texte blank pages at the back as space to create your own personal index, tailored to what’s at stake for you. You’re always reading a book with some interest, from some angle, so create an index that helps you come back to the book later and immediately get back up to speed. This might include tracking some specific themes and noting the page numbers where it appears, then drawing some lines of connection, etc. It’s also a space to perhaps summarize your taken particular issues, etc.