First of all, it consists of using an index that will be the only reference point of your system. This index allows you to create the structure of your file system but it goes far beyond.
To maintain your index you can use the note management software you want even if some are often honored like Bear and Apple Notes on Mac or obsidian.
Whichever software you choose, my advice is to make sure it can export your full index in a form easily readable by other apps. Markdown is a good example of an export format that is useful in many places.
I share @Evgeny’s opinion: just use a file system, folders in folders, and then in each folder you can have your actual documents, or just plaintext files.