It all depends. For all the tech and studio stuff, I have a main folder with lots of sub folders. They break up into user manuals, service manuals, schematics, paperwork(set up sheets, etc), and so on.
For DIY projects I have a main folder and each subfolder is a specific project: tube mic pres, tube mics, fet compressors, and so on. Each of those subfolders is a specific project containing all the necessary bobs and bits related to that project from boms and artwork to gerbers and schematics.
Because diy projects cross mingle with the studio stuff, I do keep duplicates of schematics only in both spots because the tech folder is also shared to the studio cloud in read only access. I may cheif there but I like others to be able to read and access information so they can ask questions and learn. The DIY stuff of gerbers is backed up to another drive and cloud elsewhere.