Okay, I think I figured it out.
The Overall Story is about a group of people who have all come together to figure out a way to avenge the massacred people without bringing down the wrath of the organization.
The Main Character is personally dealing with hiding her identity because she doesn't believe she'd make a good queen - she's spent her most of her life working as a mercenary. She also refuses to use the magic that marks her as the rightful queen because when she was a child, she panicked during an attack on her home, used her magic, and inadvertently caused the death of her family. So she believes that it's best to stay hidden so that she isn't put on the throne (because of tradition) and causes even more problems for the people as queen.
The Influence Character is a former teacher who has the ability to draw out people's magic, but is now a disgraced war hero. In the story, he's constantly pushing the MC's buttons, pointing out all the ways in which she's limiting herself in order to make other people comfortable. He, on the other hand, couldn't care less and doesn't let how people remember him stop him from doing what he's set out to do, which is help the MC avenge the massacred people (and also protect her, because he knows who she is).
I think the relationship between them develops because of the focus on understanding the true nature of her magic, and what it actually does. The major events that build their relationship in the story all revolve around getting a better understanding of how her magic actually works.
I know that 'Getting Revenge' is generally an Obtaining thing, but I really like the idea of having the source of conflict being not just in getting revenge, but in the way they're thinking about how to go about getting revenge. Mostly because I want the ending to revolve around them finally changing their way of thinking and cutting ties with the organization in a massive way, and the MC finally deciding to use her magic and reveal her identity (the original ending of the story.)
So... yeah... This is where I end up running into a wall most of the time. Because Getting Revenge seems to be mostly an Obtaining concern, but it feels like putting it in Conceptualizing would be a better fit when it comes to the other throughlines. And that's before I even get into the other levels.