[tilia]

If you are importing books from the Kindle, you should do it by plugging in the device, and then switch to device-view in calibre. Mark the books you want to import, and add them to the library.

Those <0.1MB-files you have in your library are probably mbp-files. These keep track of thing like highlights, bookmarks and last page read. You can safely delete them from calibre. Or you could merge them with the book-records if you want to keep a copy of them in calibre.