How do you file your notes under specific topics? Like all your
short stories are under short stories, right? How does that work?

You can use remember-planner to quickly add notes to planner files.
After setting up remember-planner according to the notes in
remember-planner.el, use M-x remember to open a buffer for notes. It
starts out with a link to the current buffer. After you type in your
note, hit C-c C-c (remember-region). This prompts you for a planner
page to associate the note with. By default, notes are added only to
today’s day page. However, if you specify something else
(ShortStories, for example), then the note is copied to that page. =)