I still keep everything from my school days sorted by class, even if digital references were provided in the class. I didn't really start developing any real organization of material until starting work. But even when I was going to graduate school part time while working full time, I just sorted the references provided by class as well. Typically if it's a useful source of information, I'll remember where I put it.
I have a couple of main folders: (Example) Calculations, Forms, Grad School, Jobs (projects from past employment), Reference Library, and Software Manuals. Organizing the calculations, forms, jobs, and software manuals is pretty straight forward since it's either not as abundant as my reference library or things like projects from past employment is obvious how to sort. The reference library is tricky and my organization isn't perfect. Some files could go into multiple folders. For me, the best thing is to make sure the file is accurately named so you can just search for it in the instance when you can't find it. I couldn't tell you how many codes or manuals I've downloaded that were named some series of numbers without any text.
The main subfolders in my Reference Library folder are: Standards (ACI, AISC, ASTM, ect.), Codes, Concrete, Conference Material, Design Manuals, Drafting, FHWA, Inspection Manusl, Manufacturer Product Info, NCHRP, Papers, Pavement Design, Seismic Design, Slope Stability, Specifications, Subsurface Investigations, Surveying, USACE, Vibration Monitoring. There are more subfolders in my Reference Library but I don't think listing them would be helpful to you.
Overtime I'm sure you'll figure out your own system. Just try to be diligent by periodically organizing your folder and back them up on a personal cloud space if you're not already doing that.