If your assignment is to annotate as you read, then you are being asked to do a complete annotation of the text.  When you actively read this way, you are reading with a pen in hand and making notes and observations in the margins.  If you are given a list of things to look for, then you should mark those examples as you notice them.  If you are asked for personal response annotations, then you should note your reactions, questions, and observations about what is going on in the story.

Specific to Huckleberry Finn I would be looking to annotate commentary about characterization, symbolism -- especially of the river vs. the land; example of verbal, dramatic, and situation irony, humor, dialect, and themes/topics such as family, loyaly, racism, adventure, right vs. wrong etc.  The book is loaded!

When you are reading for school, it doesn't mean you aren't reading for pleasure, and a lot of students don't like to annotate, but think of it as a huge favor to yourself.  You will have reference points to go back to.  You will have already collected evidence for any analysis writing you may be asked to do.  You will have notes that can help you contribute to group discussions.  Active reading takes more work, but it is almost always worth it.

For a reveiw of things to look for, you could look over the information here in enotes.  The link is below.