I agree that the Relationship Throughline feels like the least determined, but I think that might be a feature of the theory, not a bug. If the Main Character Resolve is Change, then the Relationship Throughline will change accordingly, but if the Main Character Resolve is Steadfast, then the Impact Character Resolve must be Change, and the Relationship Throughline will change anyway. So the Relationship Throughline is going to change no matter what the resolve is.
As to how the Relationship changes, I think you're given a lot of leeway in this regard. Neither the theory nor the program give you any information on this, other than the Issue, Problem, Symptom, etc. Is the relationship growing or declining in this story? Is it healthy or unhealthy? Do the MC and IC affect each other directly or indirectly? Is it a romantic relationship? Paternal? Companionable? Rivalrous? Err... avuncular? Anyways, my point is, you've got a lot you can do here. This is the heart of your story, which means it beats with the unique tempo you've given it.
*If you're not sure what type of relationship you want to choose, this might help. Confucianism looks at five Bonds: between ruler and ruled, father and son, husband and wife, elder brother to younger brother, and friend to friend. We can describe these more laconically as political, paternal, spousal, fraternal, and congenial. Choose any of these, make them positive or negative, make them growing or declining... you've got a lot of options.