My recommendation is always to start with what you know best. If that's the Main Character throughline, then start there. If it's the Relationship Story throughline (which is frequently strongly emphasized as the "romance" part of a Romance Novel), start there. The same goes for the Objective story throughline or the Influence Character throughline. Another trick is to skip the Domain level if nothing jumps right out and grabs your attention, and proceed to the Types level. Which group of four types (there are four in each class) seems to describe your story's "plot" best? If that doesn't work, skip the Types and go for the Variations. Given the context of the domain you are choosing, which thematic issues seem to be most relevant? Each Type and Variation is unique to the Class in which it is located. (This is not true of the Elements.)

One more thing to keep in mind is that the purpose of picking (or assigning) a domain to a throughline is to identify the general area from which conflict emanates. Is it a situation (Universe), an activity (Physics), an attitude (Mind) or a manner of thinking (Psychology) that is CAUSING TROUBLE for the characters?

You say that your MC "feels trapped in an unrewarding relationship". If the focus is on her physical situation, then that would imply a Main Character domain of Universe. If, however, these feelings were more due to a disturbed (or out-of-balance) mind, then Psychology might be a better MC Domain -- particularly if she is a Be-er and would prefer to change her feelings or ideas when confronted with conflict, as opposed to doing something about it physically.

Is the conflict between the MC and the IC due to physical abuse or problematic activities (Relationship Story Domain of Physics), or is it more like the conflict grows out of manipulations or mind games (Relationship Story Domain of Psychology)?

I have no idea what your Objective Story throughline is about so it's nearly impossible to make a useful suggestions. However, here's a little trick you can use to help think of the Objective Story "objectively." Think of what ALL the characters in your story are concerned with. What holds them together -- why are they even in the story. Make sure that, when thinking of the characters, you identify them by their ROLE (heroine, villain, father, doctor, sister, etc.). Avoid using their proper names. Once you think about a character in terms of their name it's very difficult to avoid personalizing your feelings about them which makes seeing them objectively very hard indeed.