How do the Issue and Counterpoint interact?
Moving through the Story Guide, I got to the part where you're asked to rate if an ISSUE or COUNTERPOINT is advantageous or disadvantageous. I'm not sure how to interpret this. I "suspect" it is strictly judged by its utility to the characters. Seems straightforward when dealing with a positive story goal.
Faux example: If I'm writing a story about a couple of guys snatching purses from elderly blind women in order to raise money to go on a seal-clubbing safari and I'm presented with a ISSUE/COUNTERPOINT of MORALITY vs. SELF-INTEREST ... well, obviously "self-interest" is an advantage and "morality" a liability. Is this the way to view it? Or, do I guage it depending on the Story Judgement (ie: the author's standard?)
(The former version is about the only way I can even envision "MORALITY" being a disadvantage.)
Is it different in other throughlines?
The evaluation of a thematic point being advantageous or disadvantageous is from YOUR (the author's) perspective not the characters'. It's so you can objectively make a note to yourself how you want they are to be seen by the audience at the end of the work. You'll most likely want to "gray" the evaluation by showing positives and negatives for each thematic point. The slider tool in Dramatica is to let you indicate how you'd like everything to balance out after all is said and done.
In your faux example with the purse-snatching, seal-clubbing safari boys, I don't see that there's any clear advantage to "self-interest" or disadvantage to "morality." Don't take for granted your values are the same as others. You must say (or show) WHY one is more advantageous than the other. It's all a matter of context. For example, in a world where seals are overpopulating the world and threatening to destroy the ocean's fish supply, the stingy woman's reluctance to part with her purse (self interest as disadvantageous) contrasts the risks the thieves run by using her money to finance a trip to club seals in order to prevent world starvation (morality as advantageous).
You're the story god. You say what is right and wrong in your story world--what is advantageous or disadvantageous and how much it is.