How do I leave a comment on a passage?

A comment is a note beside your prose that never reaches the exported book; every comment is listed in the Inspector so you can jump back to it.

Steps

Select the passage, or click where the note belongs.
Press ⇧⌘K / Ctrl+Shift+K.
Type your comment. Keep At the cursor to pin it to the passage, or choose For this chapter for a note on the whole chapter. You can also mark it as a TODO, Idea, Placeholder or Explainer.
The comment is attached to the text you selected.
Press Add or Enter. A small numbered chip appears in the text where the comment sits.
To see every comment, open the Comments, Bookmarks & Flags panel in the Inspector and its Comments tab.
Comments are grouped by chapter, each with its number.
Click a comment in the list to jump to its place in the text.
Revise the passage as usual. The comment stays with the text it was attached to.

Click a screenshot to see it larger, then use the arrow keys to step through them.

After revising, click the comment in the list and check it still points to the right passage.
Close and reopen the chapter and check the comment is still there.

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