Read excerpts from Flowers for Algernon. Google Books has a few previews of the book available, as well as several versions of plays based on the novel. Make sure you read from some of Charlie's early progress reports, as well as some in the middle and the end. It is the best way to get a true sense of his character and the contrast between his life before the surgery and after.
Look up the definitions of vocabulary words you do not already know. If you can figure out the meaning of the words from the context, that helps, but having a more thorough knowledge of those words can help you get a much better appreciation for Charlie's intelligence. You also understand better how his life changes throughout the story when you have a better understanding of what he talks about.
Immerse yourself in some study guides that help you understand Charlie Gordon and his experiences as well as what Keyes is trying to accomplish in this work. SparkNotes and BookRags offer some interesting study questions and critical essays of Flowers for Algernon.
Organize your own thoughts about Flowers for Algernon by writing your own critical essay. Describe major themes and elements that seem important to you and use examples and quotes from the excerpts you read to support your ideas. This is also a great way to practice your own essay writing skills.