I have a few different ways I organize my files:
1) I work a lot of tickets in specific source-code directories. Each directory has a .
capture.org file in it w/capture templates for TODOs and NOTES. These typically get archived with the ticket is finished
2) I also use emacs/org on my tablet for note-taking in class. These org files all go in a subdir off my Dropbox directory: ~/Dropbox/ClassNotes with a classname-date naming scheme
3) I also have a org directory off my home director (~/org) that holds all my more general org files such as more general TODO & NOTES, my daily work log file, and so forth.
But really, the big thing is that whatever order you use, that it work for you. Plus, it can always be changed later if it doesn't work quite right, or needs expanded.
Subhan