Characters and places
Research notes that know where they appear in the manuscript.
A note is a character, place or thing
Every document under Research stands for someone or something in the book. Its title is the name. The folder it sits in is what kind of thing it is, so a note in Research/Characters is a character and one in Research/Places a place; call the folders whatever suits the book.
Other names go in the inspector under Also called, comma separated: Lizzy, Eliza for Elizabeth Bennet. A name with two or more words is also known by its first or last word when no other note shares it, so Mr. Darcy is found as Darcy; titles such as Mr and common words such as Park or Hall are never used on their own. Names match with their capitals, so Bath the place is not found in a bath.
In the manuscript
Wherever a name appears in the manuscript, it has a faint dotted underline. Click it and the inspector shows that note's card; Cmd-click opens the note itself.

The card has the note's synopsis and the start of what you wrote in it, then how many scenes the name is in, how often, where it first appears, and every scene it appears in. Click a scene to go there. Back returns to the document.
With a scene selected, the inspector lists everyone and everything it mentions under In this scene, the most mentioned first. Right-click one for Show card or Open note, or click it for the card.

On a research note, the inspector shows the other way round: Appears in lists the scenes that mention it. Focus mode hides the underlines.
From a selection
Select a name on the page, then right-click it or press the research note button in the formatting toolbar.
- New research note “Mrs. Long”… asks which folder it goes in, makes the note and shows its card. You stay where you were on the page.
- Add “Mrs. Long” as a name for… lists your notes and adds the selection to the one you choose, under Also called.
- When the selection already is a note's name or one of its other names, the menu offers Show card for “Mrs. Long” instead, so a character never ends up with two notes.

The new name is underlined across the manuscript straight away.