When looking at the Story Engine it has Judgment in as an OS Plot Dynamic though its definition seems to be more concerned about the MC journey.  I was wondering why it is in the OS Plot Dynamics window when, for me, it feels like it belongs more to the Main Character window?

Short answer: No and Yes.

The Story Judgment sits half in the Main Character Throughline and half as part of the story's plot dynamics.

THE NO PART

The Story Judgment is about the resolution of the Main Character's angst. If it is resolved, that is 'good.' If it is not resolved, that is 'bad.' This is what makes it seem like Story Judgment should be part of the Main Character dynamics.

THE YES PART

Most people do not make a distinction between Outcome and Judgment when thinking about story endings. They generally think of the ending as either a happy ending, a tragedy, or a bittersweet ending. AND, they tend to associate the story ending with the part that Dramatica identifies as the Overall Story throughline.

When we separated out the Outcome and Judgment components, we kept them together and put them in the Plot Dynamics since both were associated with how the story ended. Each throughline has character, theme, plot, and genre elements, so putting the Judgment with the plot dynamics is a valid way to understand that dynamic.

 I'm developing a story where my Main Character is also my Overall Story protagonist. I'm having trouble distinguishing between Main Character and Overall Story throughlines. Would I be right to think that the Main Character throughline follows the story of the Main Character's personal motives - why they act and what they want - while the Overall Story throughline follows what they do and what results? I'm having a hard time seeing separate story lines. Clarification, especially with examples from sources I know, would be wonderful.

Here's a useful trick to help you keep the Main Character and Protagonist separated in your thoughts. Refer to the Main Character by his or her proper name: Dorothy Gale; Michael Corleone; Rocky. Refer to the Protagonist by its role: the girl from Kansas; the youngest son of the Corleone family; the wannabe boxing champion.

• In The Fugitive, Dr. Kimble is the Main Character and he is concerned with finding his wife's killer. In the Overall Story throughline, everyone is concerned with capturing the "fugitive" convicted murderer (the doctor) and putting him back on death row.
• In Hamlet, Prince Hamlet is the Main Character and is concerned with the loss of his father and how his life has lost its rudder because of all the recent changes. In the Overall Story throughline, everyone wants to forget about the unfortunate circumstances of King Hamlet's death and move on...if only that son of his would let them.
• In Star Wars, Luke is the Main Character and feels stuck in his adolescence--he's meant for bigger things. In the Overall Story throughline, the Rebellion has stolen the Death Star plans and hopes to use them to find a flaw in the planet-killer before it wipes them out.
• In The Silence of the Lambs, Clarice Starling is the Main Character and is haunted by the screaming of slaughtered lambs (and has transformed that drive into protecting the "lambs" of the world from "wolves" like Hannibal Lecter and Buffalo Bill). In the Overall Story throughline, the serial killer, Buffalo Bill, has kidnapped the Senator's daughter and will kill her and others if he is not stopped.
• In Garden State, Andrew Largeman is the Main Character and is concerned with his health (short but blinding headaches) after a lifetime on lithium. In the Overall Story throughline, everyone is concerned with reconnecting with the "famous" actor ("Hey, aren't you that retarded guy on TV?") after his mother dies and he returns for an extended weekend to attend her funeral.

The setting may or may play a major part in the OS. It also may or may not have a significant in the other three throughlines. It is purely a matter of author's discretion. The setting, as much as any other element of the storytelling, may be made an integral part of the story or just part of the "scenery." Some genres such as fantasy and science fiction and westerns tightly integrate the setting in the story. You'll notice, however, that this close integration often bleeds into the other throughlines as well. The Main Character will be a natural part of the setting, or just as frequently notable for his/her newness to the setting.

I think it is safe to say that characters, plot, theme and genre are what most affect the story throughlines. Insofar as the setting is part of those story fundamentals, it will impact how an author tells the story. It's not safe to assume that the setting will have a greater impact on the OS throughline than it may on the other throughlines.

How do you keep them from becoming separate storylines?

The MC problem and the OS problem generally don't start out having much to do with one another, but over the course of the story the development of one and the development of the other become intimately tied. So, rather than seeing a story as "a mother who has to solve a mystery but who has to get over the death of her daughter before she can do this," look at it as "a mother driven to solve mysteries because of her daughter's death cannot solve the current case because the personal, unresolved issues she has with her daughter's death blind her to the secret behind the mystery!"

Story elements only become connected when YOU, the author, make them connected. Without the connections, the story is meaningless. You must supply the meaning, and in Dramatica you begin that process by creating the storyform. After all, what is a storyform other than a tangled web of connections (relationships)?

When tying the Main Character's personal issues with the Overall Story throughline, it's best to show some sort of causal relationship between the Main Character's resolution/non-resolution of his or her personal problem, and the success or failure of the OS goal.

Examples: (Spoilers Ahead)

HAMLET -- Over the course of the story, Hamlet is changed such that he no longer sees his uncle as a threat, nor seeks to avenge his father's ghost. This allows him to accept his uncle's request to duel for his family's honor -- a duel orchestrated by his uncle and Laertes in order to "legally" get rid of Hamlet. The plot works far too well and everyone in Hamlet's and Laertes' families are dead by the play's end.

AMERICAN BEAUTY -- Lester's decision not to deflower his daughter's girlfriend sets him up to be murdered while he is alone and lost in reverie.

WHAT'S UP DOC? -- Howard receives his musicologist grant which makes him more amenable to accepting his irrational attraction to Judy.

THE SIXTH SENSE -- Helping Cole to understand what the "dead people" want of Cole lets Malcolm come to terms with his own personal problem.