hmmm each person does it a little differently
for example, although i would always read a book with a pencil in hand, i wouldnt bother doing what Studyinghard describes, but each to their own
i would read through the book, and as kyzoo said, make sure you really understand the characters, their thoughts, feelings, motiviations, influences on other characters, etc., the plot, the motivations of the author, and the themes and ideas the author is trying to portray via the plot (via the characters).
the pencil is used to underline anything which coudl a) jog your memory for the things mentioned above b) strikes you as crucial to plot or gives insight into the character, or seems 'typical' of the character or c) portrays a certain idea which you ahve about the novel particularly well e.g. The quote '[Winston] loved Big Brother' from 1984 shows the true and terrifying extent with which the Party is able to manipulate not only and individual's actions, but also their thoughts and beliefs. This parallel's Orwell's larger message, which is a warning of the inherent potential dangers to individual freedom contained in a totalitarian society.
obviously you'd never incorporate a quote into a sentence in that way, but thats what i mean in terms of quotes you would underline.
other than that, just try to garner your own opinions and views of the book, and then try to express them in an articulate essay form
