For the essay's main topic, choose subjects that -- as a pair -- lend themselves to comparative analysis and a specific thesis, while also meeting the requirements of the assignment. For example, comparing black masculinity in "The Narrative of the Life of Fredrick Douglass" and Melville's "Benito Cereno" could prove too big for a three-page paper. However, if you focus specifically on the characters of Fredrick Douglass and Babo, and their attributes as proponents of racial equality, the comparison becomes focused. The argument becomes manageable; as a result your thesis about how cultural differences affect interpretations of black masculinity and heroism becomes clear.
Of course you want to use primary sources, which in this case would be the original texts of the narratives mentioned above. Primary sources allow you to comment on the genuine article, and propose your own ideas without piggybacking off the ideas of other scholars. You also might want to consider using secondary sources. Secondary sources are other people's ideas about the original material, such as another critic's analysis of "Benito Cereno." You can treat secondary sources either as support for your arguments, or as foils that you can use as oppositional evidence against which you'll argue. Treating your essay as a conversational exchange in this way adds credibility to your argument, because you are willing to acknowledge opposing viewpoints.
You can tackle structure one of three ways. Using Douglass and Babo as examples: You can say everything you want about Douglass, and then follow with everything about Babo. The problem with this approach is that by the time readers get to Babo, they might have forgotten what you've said about Douglass, and then have difficulty following your argument. The second method is to structure the essay according to each of the thesis statement's main points and then address both characters together in relation to each point. A more advanced option is to structure according to main points, but to routinely use one subject as the lens by which you illuminate the other. For example, a main point of your thesis might be that Babo is actually noble, despite the fact that the narrator views him as a villain. You can use examples of Douglass' admirable qualities to highlight Babo's comparable nobility; in this case you've incorporated both texts into a single essay section, within the context of a main point that supports your thesis.
An outline is essentially a list of sections of your essay, including short notes that express the ideas and roles of each section. Whichever structure you've decided to use, outline the essay according to it so you can actually see the progression of your ideas, which you can scrutinize for logic, clarity and flow. If the outline shows you that the essay doesn't work, re-outline it using a different structure. This will save time as opposed to drafting the entire essay -- only to realize afterward that you have a major structural issue to fix.
Because comparative essays can get organizationally muddy, you'll want to get regular feedback throughout the drafting process. Ask your teacher or fellow students to read your drafts, with the purpose of identifying confusing information, or aspects of your argument that don't directly support your thesis. Also, outline your essay again after you've finished a first or second draft. "Reverse outlining" will enable you to see what you've actually done with respect to what you set out to accomplish, in terms of examining and proving your thesis statement.