Notes that become codex entries
Start small
You don't need a codex to keep track of a book. The notes panel in the editor is a perfectly good place for a character sheet, a map of the town, a list of rules you've made up—and notes have two things that make them a small codex of their own.
Tags on notes
Every note has a tag box in its header. Type a tag and press Enter; as you type, the codex's types are suggested—character, place, item, faction, rule, event, map—along with plot and research. A note can carry as many as you like.
Once a few notes have tags, the notes list grows a row of chips with counts. Click character and you see only the characters. It's enough structure for a standalone book, and it costs nothing but the tag.
Screenshot: the notes panel in the editor, with a note's tag box in its header and the notes list's row of tag chips with counts.
Ad-hoc connections, briefly
On the codex side, an entry also has Ad-hoc connections: simple links to other entries—rival of, visited by, mentored by—for the relationships that don't need a field of their own. If you find yourself making the same connection on every entry of a type, it's time to add it as a proper field in Setup, which gives it a dropdown and shows it from both sides.
When a note outgrows the book
The day a note wants to be shared across books—the character comes back in the sequel, the town is in three series—turn it into a codex entry. Open the note and click Make this a codex entry in its header. A small window asks for the entry type; the note's title becomes the entry's name, its text becomes the body, and its tags become the entry's tags.
Screenshot: a note open with Make this a codex entry in its header, and the small window that asks for the entry type.
If the book isn't in a universe yet, the same window asks you to Create a universe: give it a name, and the book's series (or the book itself, if it's a standalone) is put in it as part of the same step. You don't have to go and set that up first.
By default the note is archived afterwards, since the entry now holds it; untick Archive the note afterwards if you'd rather keep both. Either way the note keeps a link—Open in the codex → appears in its header—so you can always get from the note to the entry it became.
What carries over, and what doesn't
The title, the text and the tags come across. At-a-glance information—rank, birth date, affiliations—is filled in on the entry afterwards, since a note has no fields to take it from. The note's own history stays with the note.