You should use the save to disk feature if you wish to access the books without using the GUI, and without a reader device. When you save to disk you can specify how you want the books to be saved. What folder tree structure to use and how the books should be named. Very flexible. You can even modify the metadata inside the books on the fly, using plugboards. But perhaps this is not suitable for import back to calibre, since calibre only can read metadata from inside the files or from the filenames, not from the folder names used.
Some users dislike how calibre store the books and only use calibre to update their own idea of the perfect book storage file structure. They only use calibre to convert and fix the books and then save them to disk. After that they can delete the books from calibre, or keep them in calibre as a backup.
If you want a backup of the calibre library, backup the calibre library directly, as it is. That allows you to quickly restore the library if something bad should happen. Like the computer being stolen or a hd crash. But make sure you try to use the backup. Make a small test library. Make a backup. Pretend that the computer is stolen and restore the calibre library to another computer, or to another folder on the current computer.
More information here:
http://manual.calibre-ebook.com/faq....ary-management