I'm thinking one of three things. 1. Your Relationship Story is overshadowing the Overall Story in the telling-which should be fine-or 2. your Overall Story has everyone concerned with A love story while somewhere in all of your characters is a relationship that is not covered within the love story that everyone is looking at-that would be your Relationship Story, or 3. you don't have a complete Grand Argument Story just yet.
Examples for 1 and 2:
1. Your Relationship Story is overshadowing the Overall Story
A group of soldiers is helping to rebuild a war torn land. One of the soldiers finds himself falling in love with a member of a local village. Meanwhile, soldiers and villagers alike are concerned with the difficulties of building a bridge in order to make travel and trade easier for the village.
Your story would focus more on the couple falling in love than everyone's concern of building a bridge.
2. Your Overall Story is a love story while your Relationship Story takes place outside of that.
There is a couple who is extremely poor. They have a beautiful young daughter who once fleetingly caught the attention of the rich Lord's son. If the family can marry the daughter off to the rich Lord's son they will never again have to worry about money. Meanwhile, the rich Lord has not been viewed favorably in the eyes of the public lately. Everyone thinks that he thinks he and his family are too good for the common man. Marrying his son off to a common girl will change the way the public sees his family. Everyone is concerned with getting the Lords son and the beautiful young (poor) girl together.
There are lots of ways that the RS for this story could go down. Maybe the young girl is the MC and the IC is a...I don't know, maybe a magical dragon or something. And their Relationship is about building a friendship. You'd have an OS about a love story, and an RS about a friendship.
Or maybe neither the young girl nor the Lord's son are MC or IC. Maybe the MC is the young girls sister and the IC is a traveling salesman and the two have a relationship outside of the OS love story. Maybe it's a friendship, maybe a student/teacher relationship, or maybe another love story.
Don't know if any of that helps. Feel free to explain your story a bit and maybe you'll get some help parsing the Throughlines out.