The story is an allegory, and you could devote much space towards explaining the many allegorical elements. For instance, you could discuss the symbolism of the conch.

For every character, you could discuss his role.

Ralph is the central character. How does he change in the course of his novel–he goes from an almost naive role to one of hardened maturity, doesn’t he?

And what about Jack Merridew, his chief rival? You could discuss this rivalry.

What is the role of Simon and Piggy? Is Simon like Christ in any way?

Your annotations could contain your interpretations.

How is the setting relevant to the story? Could you place the same story in the middle of London or New York? Why does Golding place his story removed from all other civilization?

Follow your own instincts. When reading anything–but particularly this work–ideas come to mind. Don’t be afraid of your ideas–explore them. And write them down. Your instincts are the best guide to your annotations.