Have been using org-mode for a few years now but never reached the point where I would feel comfortable. I can't find a good way to organize my files, there are at least 20-30 files in my Dropbox, some are empty, some contain random notes.
Have you tried org-capture? It's nice to have the files be accessible through keyboard shortcuts, but it has the additional benefit that the potential places I could drop some random note are specified in advance, forcing me to maintain some level of organization.