Once you have the basic skills of reading and developing opinions, you need to fully understand and respond to other authors' arguments. In order to do this, you must make use of annotating for purpose, meaning, and rhetorical devices. This may seem a little overwhelming, so I'll break it down. The purpose of a text is what the author is attempting to do or persuade someone to do. For example, the purpose of this blog is to explain to potential AP Lang students some of the skills that they will need, and hopefully to persuade them that AP Lang is an enlightening course that they should take. The purpose of a given writing will help determine how the author is approaching their topic and what the overall meaning of the source really is. That brings us to meaning. This is the main idea(s) that the author proposes or discusses. You can interpret meaning from what the author explicitly states and what is implied from the tone and organization of the passage. Lastly, rhetorical devices are the tools that a writer uses to add emphasis to their writing and persuade their audience that they are correct. Examples include exaggeration, sentence structure, imagery, and many other similar grammatical uses.
Here is an example of my own annotation of poetry, so that you get a sense of how it is done.
These three overarching themes -- purpose, meaning, and rhetorical devices -- are tied together when you annotate a text, specifically looking for the use of these items. This gives a close reading of the text and allows the reader to have an easy "study guide" when they look over their annotations. Nick Otten, of Clayton HS, Clayton Missouri, explains several reasons for developing effective annotation skills and outlines several easy ways to make your annotation better (Nick Otten, How and Why to Annotate a Book).