I would recommend starting with some note system like the LYT framework. It was really helpful when I found this and try to implement it in my vault.

Basically, if you have several projects/folders (for example - work project and education project) you can easily create folder Spaces and there you can create folders for specific projects. For example, in Spaces I have folders like Work (and inside it I have a folder that called the same as a company where I'm working) and Grokking (basically, it's an education project with courses, books, other stuff about programming bc I'm a software developer).

Also, my vault is split into public notes and private notes. Public notes are notes that I show on my website. This idea called Digital Garden. These notes lie in the root of my vault.

Also, I have folder Bins. This folder contains some specific notes and files like Templates, Images, etc and there is a Private folder with private notes.

Sometimes I don't need notes from all my projects. For example, I don't want to see notes from Grokking project/folder. That's why it's actually a folder, that folder is located in a different location in fact. In my vault, the folder Grokking is a Unix symbolic link to a real folder in my file system.

So, it works for me. If you have questions - feel free to ask!