I am assuming if you are using dropbox for backup you have an existing calibre library on your PC?
If you don't than how are you keeping your books organized? I understand that your system works for you as you have done itthis way for a reason.
Calibre has to keep files in a very consistent manner because of the many many functions it performs. The developer settled on one which works for calibre and his methods.
It does not suit all users but 90% or more are happy with it once they get over the initial horror that it is not how they might do it given a choice. Possibly several of these methods might be slightly better, possibly not.
My advice is to maintain your own structure but maintain a calibre library on your computer as well for a while. Use it for a month or so or until you find a better option.
Calibre library is really zero user maintenance for the file structure other than importing and organizing your books and documents. And if you decide not to use it pretty easy to delete.
Life is too short to worry about disk space and cloud space is getting cheaper too
Helen