There is not much to configure, on purpose. This page lists what there is: the editor, the global default vault, and the per-vault file that holds views, document settings and site settings.
Your editor
ntropy opens notes in $VISUAL, then $EDITOR. It won't guess a default: if neither is set, opening a note fails with a message saying so. Set one of them in your shell and ntropy uses it for new, today, and opening notes from the picker.
Your default vault
ntropy init --set-default records a vault as the global fallback, used when nothing nearer resolves (see Finding the vault). It lives in a small TOML file in your OS config directory, ~/.config/ntropy/config.toml on Linux and ~/Library/Application Support/ntropy/config.toml on macOS, holding a single line:
default_vault = "/Users/you/notes"
You'll rarely touch it by hand; --set-default writes it for you. Without that flag, init never touches the global config.
Per-vault config
Each vault has its own <vault>/.ntropy/config.toml, so settings travel with the vault rather than your machine. Views are the main thing in it, one [[view]] table per view:
[[view]]
name = "by-tag"
field = "tags"
[[view]]
name = "by-status"
field = "status"
The ntropy view commands manage these entries for you; Materialized views has the whole story.
The same file holds two optional tables. [render] sets the Typst theme and the paper size for rendered documents; see Document themes. [site] sets the site theme, the front page, the title, the language, whether pages list related notes, and the sidebar's root; it also takes [[site.nav]] tables for a hand-assembled sidebar and a free-form [site.vars] table that the site theme's templates read. Exporting a website covers every key.
Every key of both tables is optional, and when ntropy writes the file it leaves out a table whose keys are all at their defaults.
Templates are not configuration. They are files under <vault>/.ntropy/templates/; see Templates and daily notes.