There are no hard and fast rules about organizing a comparison/contrast paper, of course. Just be sure that your reader can easily tell what’s going on! Be aware, too, of the placement of your different points. If you are writing a comparison/contrast in service of an argument, keep in mind that the last point you make is the one you are leaving your reader with. For example, if I am trying to argue that Amante is better than Pepper’s, I should end with a contrast that leaves Amante sounding good, rather than with a point of comparison that I have to admit makes Pepper’s look better. If you’ve decided that the differences between the items you’re comparing/contrasting are most important, you’ll want to end with the differences—and vice versa, if the similarities seem most important to you.
Plan B: Use Plan B if you have only a few, larger similarities or differences. After your introduction, in the next paragraph discuss one similarity or difference in BOTH works or characters, and then move on in the next paragraph to the second similarity or difference in both, then the third, and so forth, until you're done. If you are doing both similarities and differences, juggle them on scrap paper so that in each part you put the less important first ("X and Y are both alike in their social positions . ."), followed by the more important ("but X is much more aware of the dangers of his position than is Y"). In this format, the comparing or contrasting goes on in EACH of the middle parts.