The best place to start, when writing any essay, is to brainstorm everything you know. Typically, when an assignment says to "compare" two essays, often what the prompt really means is to compare and/or contrast. Depending on what your assignment specifies, I would start by making a list of subjects or themes that are similar about each book. Because the books have such different plot, my advice is to stay focused on the major similarities between the books and only highlight minor differences within those (which will be obvious once you get started).
One good starting place is to look at the characters in each novel. Both books revolve around male protagonists who attend a prep-school. Both books show the major changes and growth of these two protagonists in a relatively short period of time. While Gene suffers from a competitive and jealous relationship with his roommate Finny, Holden also deals with competition and jealousy towards the world. You could probably make a case that what Gene dislikes in Finny, Holden also dislikes in others. You might even be able to bring this to say that as a result of this internal conflict, both are very lonely characters.
If you take these ideas and keep going with as much brainstorming as possible, hopefully you will generate plenty of ideas to choose from, making the organization of your paper come very naturally. Good luck.