Characters have a way of developing their own relationships with each other. This is one of the most fascinating aspects of writing a novel. Interactions that you never anticipated begin to develop and start to shape a story in unexpected ways.
When planning a story, you think in terms of connections. These characters are siblings, or lovers, or enemies, etc. A story can be hatched in those terms, but what those terms inevitably mean become complicated. For me, the earliest chapters of a manuscript are a way of establishing these relationships.
It can be painfully complex and slow at first, but once I've figured out how two important characters relate to each other, it makes everything that comes after that much easier to write. Motivations for their actions become second nature and even their reaction to situations is easier to see. I'm happy to say the two main characters in my new manuscript have reached a level of comfort with each other that should allow me to move forward smoothly.