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The driver looks for files under the books folder in the main memory. All books there will be listed. Move your builtin books into that folder if you want them detected by calibre.
As for 2 and 3 that is a device issue, all calibre does is put the files on the device, after that, it's upto the device to read the metadata from the files and present a list of books to the user. You should try posting in the pocketbook forums for help.
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