If you have a moment, could you please help me understand the best order to write up Throughlines?  I have been starting at the top, Domain on down to Signpost 4. When I get to Problem, I realize I have not yet set up the problem properly.  If we were to number the Story Points from 1-14, what would be the best order to write them?  It seems PROBLEM should be #1, then what….?  I would GREATLY appreciate your help in understanding how to best attack these Story Points, as to the order they should be written (at least in general).

It doesn't quite work that way.  The only story points below that have a specific order are the four signposts.  Each of the other story points should be illustrated at least once within EACH signpost.  This means that by the end of MC Signpost 1 (Act 1), all of the MC story points are illustrated at least once (if not more). 

Which story point to illustrate first?  It depends on how you like to write.  However, here is another way to look at each of these story points:

• DOMAIN:  This is the most genre-like and broadest aspect of the MC's throughline
• CONCERN:  This is more plot-like and may be considered to be identified as the area in which the MC's personal goal exists
• ISSUE & COUNTERPOINT:  These are the most theme-like as they relate to the MC's throughline
• SYMPTOM, RESPONSE, PROBLEM & SOLUTION:  In a character-centric throughline, these are the story points most associated with character development.
• UNIQUE ABILITY & CRITICAL FLAW: These story points tie the MC throughline to the OS throughline, so they seem both thematic and plot-like in nature.
• BENCHMARK:  This story point indicates how progress is measured in the MC's development.

So, depending on your preferences, you may focus on the more genre-like, plot-like, thematic, or character-related story points first and then progress from there.  Or, mix them up in any order you want, so long as they appear within each act/signpost.

Using the gists my Relationship Story Domain comes up as "Considering Something Unacceptable". When I look at the Theory information is says "the heart of the problem" and "this describes how the MC and IC relate to each other in the story". When I look in All Topics to the left and click on Relationship, this Considering something unacceptable shows up in RS Domain, not RS Problem. When I click on RS Problem, the only choice is Equity.

Would that mean they start off thinking each other's attitude/response is unacceptable, then the IC changes? Does the IC change if the MC is steadfast, or does he just fade away? Would it make sense for the IC at the end to consider himself kind of equal with the MC, giving him a tip that saves him, before fading out?

It's a matter of scale. As a domain, the main conflict in their relationship will be a clash of attitudes in terms of considering something as unacceptable. A RS Problem of Equity means that the heart of the conflict in the relationship grows out of equity (fairness; balance). For example, a married couple come into conflict in their marriage when everything has to be completely even (if one set of inlaws stays for two weeks, the other set of inlaws must stay with them for two weeks (even though neither of them can stand spending time with one set of inlaws) in an effort to be fair.

If the IC is change, the MC is steadfast, and vice versa.