Now that you've done some good analysis within your paragraphs, it's necessary to examine how they fit in to the goal of your overall paper.
Avoid chronology
When looking at your paper as a whole, it is much better for your paragraphs to relate according to a process of thought, rather than of chronology. If it seems as though your paragraphs are divided according to the order of your source (In other words, "first this happens," then "this happens," then "and finally..”), there's a good chance you're lapsing into plot summary.
Ordering according to thought process
Here's where your highlighting becomes useful again. Follow each of the ideas you developed throughout the text individually.
If you highlighted in different colors, make all your pink highlights one section, your blue highlights another, and your yellow ones a third. In this manner your writing flows in an ordered progression, but according to the development of an argument, rather than recapitulation of the text.
Make your paragraphs build off each other
It's best to try to arrange your paper in a manner that grows increasingly more specific. In subsequent paragraphs, try to refer back to what you mentioned in previous ones, and explain how your current subject extends or re-examines it in a new light.
Transitions
In order to give your paper unity and flow, it's important to always make smooth transitions between paragraphs. Consider the relationship between the two paragraphs, and use it as a way of moving from one to the other.
You might address a similarity in argument, by saying "In a similar manner...", "This argument may be allied to "subject B" in terms of... ", "Likewise... ", or "The idea of X recurs again with respect to... ".
To express a dissimilarity, you might use "In contrast...", "On the other hand... ", or "Nevertheless".
