How to organize files?

When to upload to Dynalist? When leaving in the file system? For what reasons?
If Dynalist is the leading system, I can put all of my files into one folder and link them, or not? For what do I need a seperate folder structure in my file system?

I don’t use Dynalist as a file system, and I don’t think it should be used as such. I only upload files when my topic requires more information, like a screenshot, and they never “leave”.