As I write, I keep my plot notes above the Manuscript in the Binder. I personally have two plots going in my book, and I keep two plot notes docs.
Through trial and error I have discovered that writing in notes and bullet points in the normal way makes working with them awkward and difficult, because I have to scroll down and down and down … more and more as time goes by.
So now I work upward. So my most recent notes are at the top. I put the month/date for each time that I add some extra notes, and insert a horizontal line above each set. This also helps if I open them in a quickreference window in edit or compose mode.