information is generally recieved and produced digitally e.g. .pdf .xlsx .doc or even images. for handwritten notes this can be captured as well as a image file 
and possible via OCR word doc.

for each subject consider logical separation:

1. course material - any material given to you consider setting up subfolder for each topic.
2. homework - homeworks that require you to write and submit something agai by topic if it makes sense
3. supplimentary material- material/notes you have researched as part of your work/revision by topic
4. quizes(flashcards)/extra problems - as part of revision you may want to create physical/digital flash cards