The PSR is supposed to represent the subjective view of the story; i.e. how the story looks from within the minds/perspectives of the characters. The idea is this: The signposts/variations of your story will be explored as identified in the story structure chart. However, to the characters, it will FEEL as if they are progressing through the story in the order identified by the PSR. If you successfully portray the subjective experience of the characters according to the variations identified by the PSR, your readers will intuit the correct storyform that is operating underneath.
So as a writer, use whichever view is more useful to you in the moment. You as the author get to see the "true" act/sequence order as identified by the story structure chart. The characters do not. Sometimes it is helpful to think: "Ah, these characters THINK they're struggling with issues of the Denial, but I know they're really struggling with issues of Perception in this scene!" Other times it's more helpful to look to the variations identified by the PSR so as to better portray story events from your characters' points of view.
So to summarize, the PSR is helpful for trying to figure out how to translate the storyform you've identified into a temporal progression that "works" in the minds of your readers, because it identifies how the issues explored over the course of the story will appear to your characters. Neither view (the story structure chart and the PSR) eclipses the other. They provide different views on purpose, so as to help you write the story YOU want to write.
As to your ACTUAL question, it's important to remember that the elements you've assigned to your characters in the Character Builder screen apply only to your objective characters, all of whom affect only ONE of your throughlines directly: the OS. The MC and the IC each have their own complete set of sixty-four elements, which they represent by themselves in their respective throughlines. It's confusing because the story structure chart identifies the elements that "make up" each of the variations in ALL the throughlines, but the OS character assignments aren't made to cover variations outside of the OS.
But as for those variations within the OS, how should you handle exploring those in relation to the character elements you assigned? Well, think about it like this: all the elements are assigned in relation to the overall story goal. Some characters pursue it, some avoid it, some do x, others do y. So throughout the story, orient your objective character's reactions/actions towards that goal. But let your intuition guide you. As you write the story, allow the objective characters to speak up for the elements they represent as you see fit: i.e. When someone needs to represent the voice of reason, let the reason character speak up. Etc. etc.
I'm sure you've noticed that the story structure chart goes a level deeper than the PSR, which does not provide you with the "elements" that subjectively belong in each scene. This is intentional, a decision made by the Dramatica creators to prevent writers from attempting to write the "perfectly structured story." It is up to YOU to determine which characters belong in which OS scenes from a subjective POV, as well as what those scenes will entail.