We refer to them as substories because they can have plot, character, theme, and even genre elements.

The best way to deal with substories in Dramatica is to create a completely separate storyform for it. Then, when you go about creating the finished work, use your storyweaving skills to thread the story and substory(s) together. Substories are particularly good devices to get yourself out of a character or plot corner. Objective characters do not change their characteristics over the course of a story -- they don't grow within the context of the central issue of the Objective Story throughline. However, change the context and they can behave however you want them to.

For example, in Star Wars, Han Solo is an archetypal Skeptic--he disbelieves and opposes everything. The only time he behaves differently is when we pop into his substory concerning Jabba the Hut. Then he is very willing to help--whether it's getting ObiWan et al off of Tatooine, or rescuing Princess Leia from termination. Proper use of substories can really spice up otherwise predictable stories.