So what I've got is an MC that meets the IC at the end of the first act. I planned on it all being about showing the ICs influence, and my RS notes would have had a few scenes that were separate from this, and dealt more with their working relationship. But now I'm thinking those scenes would just drag out and take away from the pace of the story.
But as I thought about how to explain those scenes to you, I began to see more and more how the RS can fit pretty well into the IC scenes I've already got. It's no longer going to look like an independent RS story the way I wanted (and like @Gernot explained), and it'll mean abandoning the hours and hours and pages and pages of PSR notes I worked so hard on, but at this point, those hours and pages are just a drop in the bucket for this project. So if it works better, it works better. Besides, at some point, I guess it's going to be time to put down the Dramatica and write the story I want to write.
Instead of explaining the scenes I couldn't work in, though, I'll share the scenes the way I see them now.
Trying to make it as short as I can here. The MC has a fear of death (MC Domain of Mind) which causes him lots of problems. Most notably, he sees the ghosts of his dead brother and many of his dead patients (he's a cardio thoracic surgeon). There's a nurse in the hospital where he does his surgeries who was "born with a veil over her face" (a phrase that means the placenta didn't break when she born) which is the reason her mother gave for why she has "the sight" (meaning she can see the supernatural--Sixth Sense-style ghosts, demons, etc...as an aside, this character and much of the rest of this story is inspired by a supposedly true story I was told by a person I know). The IC is seen as a bit of kook because she's the one that tells everyone that the supernatural is real. I was previously seeing the RS as being about the MC, the surgeon, at the top of his field, has authority and knowledge, and the nurse who is much farther down the chain and subordinate to the surgeon, and how it changes so that the IC, having insight into the supernatural realm, would become the one with authority and knowledge. It was going to be about the struggle for the IC to be taken seriously by the MC who thinks his ghosts are all in his head--like Russell Crowe's character in A Beautiful Mind seeing the characters that follow him around (spoiler: they're not just in his head). So the scenes I outlined were going to show the MC at work ordering the nurse around and such.
(The way I explained it above is starting to feel Situation-y, like the relationship is about who has status or something. That's not what I was going for. It's supposed to be more about them manipulating each other. The IC doesn't like seeing demons and ghosts and the MC kind of tricks her into leading a seance in his house for him. He wants to see if there's anything there, but acts as though he thinks it's all a big joke. She knows she can't tell him how to do things because he's not going to listen to her, so she has to kind of play along and let him see his plans fail before kind of tricking him into doing things her way).
But now, after all the advice from this thread, I think the RS, at least in the first act, can take place in the same scene as the IC scene. Sign Post 1 for the RS is about Conceiving, so when the IC tells that MC that she knows he's haunted and he denies it and tells her she's nuts, this can be about how the relationship is...not sure how to word it exactly...how the relationship is conceiving what the problem is with the MC, conceiving of...how to deal with it...well, not sure how to say it. Anyway, the important part is I know what i'm going for, you know, in my mind, and I feel like I can write it and I'm super pumped about it now!