Also for this part:
So, there are certain things that happen in your story that you think of as part of the RS, like a big breakup scene or whatever. (This is a shortcut, because the RS is really a perspective – it views that breakup event as mattering to the relationship. But it’s an easier way to talk about it.)
It’s definitely true that the events in the story that are connected to the RS, like the breakup scene, can affect the MC and IC throughlines and “motivations” as you said.
But with Dramatica, it’s better to keep things separated and not consider the RS itself as part of, or directly affecting, the other throughlines. The myriad connections happen afterwards, once all the throughlines come together in the actual story. (With exceptions like Crucial Element and Unique Ability that do connect certain things at the narrative structure level in very specific ways.)
Once you’re drafting that story (incorporating story-weaving and storytelling), and all the characters are running around in it and doing things like breaking up with each other, now you’re operating at a level where EVERYTHING from characters’ thoughts and motivations to world events are all bouncing off each other. This is where, in both drafting and revision, it can be extremely useful to consider the throughlines as perspectives that are only concerned with (see) certain things, and utterly unconcerned with (don’t see) anything else.