The best thing to do when writing such an essay is to go through the play and identify the scenes where characters are deceiving one another. If theme is best expressed through character reactions and behavior, as Aristotle claims, then finding the deceitful moments will likely prove the most helpful in crafting an outline to follow.
For example, the crux of the plot is Don John's deception of the heroic characters in regards to Hero's virtue. He plants gossip that she has been taking lovers, which scandalizes her fiancé Claudio and causes him to violently break off their engagement.
Now, when writing this essay, your professor likely wants you to make an argumentative claim about the theme of deceit in the play. It isn't enough to say Shakespeare wrote a play about deceit: the real question is, what is he saying about deceit in particular?
Going back to the example of Don John's deception, what does this element of the story say about how people behave when deceived? Claudio's cruelty in humiliating and rejecting Hero suggests that Shakespeare believes people are easily duped, since Claudio should (by all accounts) know better.
Or perhaps the existence of many kinds of deceptions calls into doubt whether or not deception is of itself wicked? Think about how Benedick and Beatrice are tricked into thinking one loves the other—only for this to be the catalyst for their getting together.
All of this will come more easily once you have that argumentative thesis statement. That will be the beating heart of your paper. So, examine the deceptive moments in the play and decide what you think Shakespeare is saying about deception through how the characters deceive one another and themselves.