Great debates rage as to whether stories have single, multiple or co-protagonists. For example, there are arguments that Romancing The Stone (1984) has a single protagonist (usually decided to be Joan) or co-protagonists (Joan and Jack).
These arguments and problems are usually better solved by looking at characters through the archetypes lens and remembering that a core purpose of the characters is to change.
For example, it's more useful to look at one main character as the hero and the other main character as a supernatural aid.
So, how does Jack (Supernatural Aid) help to change Joan (Hero)?
The other way around, how does Joan (Supernatural Aid) help to change Jack (Hero)?
That way you can see that the process and structure is the same as any other story. That it's almost irrelevant arguing who the protagonist is. That it's all about creating a set of circumstances where the characters are forced to change. And that one main character is really the other main character's tool for doing that.