My personal view is that it is not possible to finally decide about the way of arranging or structuring your notes before you start taking notes. Because if you then realize that this might not be the “right” approach this could lead to frustration… 
So I would advice to start as open/flexible as possible. Don’t create too many folders and subfolders, don’t think too much about directly linking your notes. Maybe just start with two folders: “work” and “personal”, for example. Write your notes and use tags. This way you can easily find any note you have ever taken on a given topic - and the advantage of tags is: you don’t have to decide where to put your notes. And they help you to build relationships between your notes.
After some time you will get more and more of an idea how to formally arrange your notes, if it makes sense to build some subfolders or not, where to put direct links etc. This is my experience, at least.