I do not believe you are any more confusing than the rest of us are. And yes, it will be me to correct you, but I don't think there is much to correct.
To answer your questions:
The reason for Fredrick coming to the army group has not been decided as far as I know. Perhaps both reasons together. I don't think it matters. It is up to the author who writes it.
How the army group leaves (with or without permission) also has not been decided. We can go either way, once again. Leaving without permission, though, would be more complicated. At some point the army starts using the spies. When do we want to bring the spies to the fore? Early or late. If it is late, then Luke/Lewis can leave without permission because we will have time to tell the story.
I agree that the spy group (not in court) should spy on field movements or something else non-court related. They may find themselves in trouble again, which may be why Fredrick goes to the Elliots. Is Jon unable to help the girls? I would think so.
Two or three stories ... yes, this is where it gets confusing ... mostly because we are talking about something so far in advance.
Here's how I see it at present. The second battle that we have spoken of would happen in Masquerade whether or not we stretch this thing out into a trilogy. It would be at the tail end, though.
If we do have a trilogy, Jon's fake death would not be a part of the second battle. It would happen at the end of the second at the tail end of the war.
The story line for the third would be soemthing that brings the group back together including Jon. Does Jon come out of hiding himself? Do the rest find him? Or, soemthing else? At this point, I don't think it matters.
Zills ended her previous chapter describing the general outline of the three stories as I see it happening, which we can go with or not. Jon marrying Katrina and his fake death would happen in the second. If we go with only two stories, the marriage and fake death would happen in the first. I think going with only two might rush us some. With three we can take our time, adding bits here and there as we think of them.