The Dramatica software only allows you to develop a story with one main character per document. Some complex novels and films have more than one story going on at the same time. To accommodate this, I suggest creating a document for each of the stories. Develop each independently while keeping in mind how they will eventually be woven together.
One thing to keep in mind is that Main Character throughline in a story is different than the "writer's voice," the choice an author makes in determining how she will relate the story to the audience. In other words, you can choose to describe any event from any throughline from any character in that throughline's perspective in the first (I), second (you/we), or third (he/she/they/it) person's voice.
The reason I mention this is because several novelists use the technique of adopting the first person for many characters in their story (Stephen King comes to mind), even though most of them are merely characters in the Overall Story throughline. Sure, we get into their head a bit more and they may even be the main character of their own little substory, but the fact that the author has chosen to describe a bit of the story from their first person's perspective does not make them the Main Character of the story.