@fly2spring, Here's what goes on in my mind when I develop these two throughlines in a story...
I always keep in mind that I want two completely different stories that weave together somehow.
The MC/I is a story about how the Impact Character is trying to get the Main Character to change, whether she realized it or not.
I go so far as to pretend in my mind that I am writing a stand alone story about that relationship.
[a puppy who is always affectionate, and always "forgives" the little boy who is mean to it]
Then I try to create a completely different story about the impact character that may not even touch the Main Character directly, but whose actions will ultimately have a profound impact on the main character.
[wide-eyed puppy's adventures as he discovers new exciting things in the world... and chews them to pieces.]
In the MC/I, there would be journeys and signposts as the little boy's cruelty cause consequences like trips to the vet, spankings from parents, and etc., while the steadfast puppy comes back unconditionally loving the little boy, which erodes his cruel nature over time.
The IC story, even though filled with humor, excitement, and wonder, definitely has an impact on the little boy, even if he is not around since his toys are being chewed, and his rug is being soiled.
Anyway, I treat them like different stories, and as soon as the IC story begins to sound like another version of the MC/I, I change things.