There are a couple of different ways to answer your question.
A Dramatica Story Expert document is designed to explore one story per document. Therefore, you could create three separate documents--one per story.
Since Dramatica Story Expert is not a place to write your finished work, this is often OK for most writers. With that said, it is important to note that Dramatica sees each complete story (Grand Argument Story) comprised of four different but interconnected "throughlines." In "Hollywood-esque" terms, these might be thought of has the "Head" line (the "big picture"), the "Heart" line (a relationship of some sort), the "personal or Main Character" line, and the "Opposition" line.* What most people think as optional (such as "A" line and "B" line stories), Dramatica sees as essential.
SO....if your story is TRULY composed of three separate Dramatica stories, then you'll have a truly complex (and potentially rich) novel involving multiple main characters, multiple opposition characters (or what we call Impact characters), multiple major plots with different goals, and multiple relationships explored between your Main and Influence characters.
If not, you'll still have a more traditional story with four throughlines that all work together to make a single argument.
* In Dramatica terms: the Overall Story throughline, the Relationship throughline, the Main Charcter throughline, and the Influence Character throughline.