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.
For a shorter paper, the above might represent three paragraphs; if you are writing a long paper and have a great deal of information, you may choose to write about each point, A, B, and C, in separate paragraphs for a total of six. However you decide to organize, make sure it is clear why you are examining this subject. You might be able to compare apples and oranges, for example, but why would you? Include any insights or opinions you have gathered. And yes, in general, three is the magic number. While there is no hard-and-fast rule that precludes creating a paper based on two points, or four, or five, a three-point discussion is manageable, especially for complex or abstract subjects. At the same time, a three-point structure helps you avoid oversimplifying, especially when addressing controversial topics in which discussions tend to become polarized–right or wrong, black or white, for or against. Three-point treatments encourage discussion of the middle ground.