Pace yourself. Figure out how many pages you have and how much time you have to proofread the manuscript. From there, estimate how long it will take you to read a chapter twice, making the proper notes and edits the second time through. Finally, establish a schedule that incorporates these factors. For example, if you want to proofread a 12-chapter book in 3 months, plan on proofing one chapter a week. Dedicate chunks of time throughout the week to getting the task accomplished.
Read first, edit later. When proofreading the manuscript for the first time, do not stop to correct spelling, grammar and punctuation. Enjoy the work as a reader, and consider reading it aloud to hear how the words flow together. In this step, it is not important to stop and correct every mistake. Instead, highlight the passage in question and return to it later for an edit.
Edit clearly. Use different-colored ink or use tracking if proofreading the manuscript through Microsoft Word. Consider how other people would interpret your edits at a cursory glace. Does an edit make sense? Does it convey the essence of the remark you are trying to make? Does it require further explanation?
Go beyond the edit marks. In the margins of the manuscript or on a separate sheet of paper, take the time to hash out thoughts on character or plot points in further detail. Also use this space to explain edit marks in the passages that require further explanation. This is also a good place to point out repeated errors or patterns of thought or language that require further examination.
Weight remarks carefully. Don't just shoot from the hip when making critiques. The person on the other end takes her work very seriously and has trusted you to use good reason when making a critique. Do not proofread someone else's work when you are pressed for time or in an inordinately stressed or foul mood. Give yourself enough time to mull over the remarks, to make sure that they truly require the attention of the writer. On the other hand, your first instinct will often be spot-on.