When you are looking to re-organize your digital files (or just plain organize them), the best way to start is by looking at your highest level organization on your desktop/laptop device. For me, I want to have everything in Dropbox, so that it will be available to me on my other devices. This means going into Dropbox and setting up new highest-level folders to begin the process.
The number of highest-level folders is going to depend on how I mentally think of my files, minimizing the situation where I can't quite figure out which folder I would put the file into. For instance, my computer usage is divided into essentially 3 things: my full-time job, my genealogical activities, and everything else (mostly home/personal files).
In addition, I need at least one catch-all folder to put things that I haven't yet filed away. This is like the physical inbox on your desk, or your email's inbox system. Because I want that one at the top, I like to name that one using an exclamation point, so that it will automatically sort to the top.
So this gives me 4 highest-level folders:
Work (or the name of the place I work)
Other (or Misc)
And once I have created those, I need to move all of my existing folders and files from the topmost level to one of those folders.