Save with media: Cmd+S or File → "Save with file" — saves the project as .pmix (JSON) and copies referenced media into an _media folder next to the project file, using relative paths so the project is portable.
Save project only (PJ only): File → "Save PJ only" — saves only project data (scenes, settings); media paths are written as relative if they are already under the project directory.
Note: When moving to another machine, use "Save with file" and copy the whole project folder including _media. If media is missing on open, ensure paths are valid or replace files manually.