Now read the text again with pen in hand, prepared to do some serious marking this time around. This will involve a slower re-reading. Notice that you do not annotate (or highlight for that matter) on the first reading. Doing so tends to produce wanton, or indiscriminate, marking and highlighting, and the pen and highlighter tend to become pacers leading you through the text and turning a nice white page into a nice yellow one. Don't deceive yourself into thinking that this sort of activity is what is meant by textbook marking!
Before you start this more careful re-reading, return again to the questions you formulated after your initial survey. Develop a shorthand for your annotations, perhaps always using a double underline on the text to indicate a thesis or main focusing statement. Try writing marginal summaries as you go along as well, since the ability to summarize a text is the surest way to show your command or "ownership" of the material. Also, respond intuitively in the margins; after all, your feelings as you read are important and sometimes provide the most important insights, even suggesting your overall reaction to the text. The more you interact with the text the better able you will be to do your response to it. You will know the text well.