Subject-by-subject (or block) style: Create a series of body paragraphs where you say everything there is to say about the first subject, and then move on and make all the points you want to make about the second subject. Make sure the topic sentence in each paragraph lets readers know what the focal point is for the paragraph. Readers should be able to tell if you are talking about Viewpoint A or Viewpoint B, etc.
Point-by-point style: Rather than addressing subjects one at a time, use this style to talk about one point of comparison, regarding each viewpoint, at a time. For instance, if you were doing a comparative analysis of two leading computer companies or products, you might devote a single paragraph to a compare/contrast of pricing, then another paragraph to compare/contrast of user friendliness, and so on.