Your reactions as an Informed Reader are very important to the author. You're representative of a certain class of reader and, as such, are qualified to tell the author what you do or don't like about her or his story. At the very least, this kind of feedback is invaluable to the author. Well, you can do a critique in many different ways. The actual process you should use will vary depending upon what feels comfortable to you.
Some people read the work through and critique all in one pass.
Try different ways. Figure out what works best for you. This starts the critique off on a good note, helps maintain a balance, and ends the critique on an upbeat note. Most authors appreciate this approach. This will let the author know if he or she has set the reader's expectations appropriately.