I don't know if this works for the Cooler, but on the Cybook, you can put the Sub-path into tags. It works like this: You put a tag containing a slash ("/", but obviously without the quotes) as first character, followed by the path you'd like the ebook to be in on the device. Use slashes instead of backslashes for subfolders. For example, if you had a collection of works by, say, Shakespeare, you could put "/Shakespeare" (again without quotes) as a tag, and Calibre will put it in a subfolder called "Shakespeare". For multiple folder levels use tags like "/Shakespeare/plays".
There is one caveat: Calibre uses the first tag beginning with a slash that it finds, so to be on the safe side, just use one of these per book.
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