Write your note in the scene, highlight it, and select 'Section' from the pop-up menu. You can then set the Section to be invisible from the AI. I then highlight my text in purple so the section shows up in the plot line on the right side of the screen.

Elated Otter There's a problem with this way though -— I think your notes will be counted as manuscript's words. I have to create a feature request, so that when you exclude a section from AI, it shouldn't be counted.

I prefer another way to make notes - using additions. You can create a codex entry "Notes" then add additions to it in the manuscript. The additional advantage would be to be able to check all your notes in one place - that codex addition. Also in the matrix view.