Use a small system you can keep using
You should be able to decide where a note goes without stopping to redesign the notebook. Begin with a few folders and adjust them when the contents give you a reason.
Separate capture from filing
Use an Inbox for quick notes, scans, and shared links. Review it at a regular time. Give each note a useful title, add missing context, and move it to a project or reference folder.
A simple starting structure is Inbox, Projects, Reference, and Archive. A course notebook may instead use Lectures, Readings, and Assignments. Choose names that match what you will look for later.
Use folders for location and tags for themes
A folder gives a document a primary home. A tag lets you find material that crosses several folders. Use a small set of tags, such as to-read or a recurring subject, rather than repeating the folder name on every note.
In Memobound, saved searches turn those filters into smart collections. A collection of unfinished tasks can span the notebook without moving the source notes.
Use links for context
A project index can link the brief, meeting notes, references, and decisions. Add a sentence beside a link explaining why it matters. Backlinks help trace where an idea was used.
Prefer a link to a duplicate. Two copies of a changing note create another task because you have to remember which one is current.
Archive completed work
Move finished projects out of the everyday view, while keeping their notes searchable. Archive is not the same as delete. Make a backup before removing anything you might need again.
Review the system when finding a note takes too long. You do not need to reorganize the whole library because one folder has grown.