Similar to what they have in Scrivener. I like to make notes in the right as I'm going, especially if something I've written means I have to go back and change something else earlier in the story. The card would be specific to the chapter doc. Then when I am ready for revisions, I just go through all my notes and make the changes I wanted. This saves me from having to click out of the scene and as I end up getting out of the flow.

Example: My character is kiddnapped. I decide she could leave a gum wrapper like a breadcrumb for the hero to find later. So I make a note in the comment box to have her pick up the package of gum when she picks up her keys, back in chapter 9.

As I incorporate my edits I delete my comment. When I am done with my edits I quickly flip through my notecards to make sure I didn't miss anything. Nothing huge, but super helpful.