Hello,
Yes, you can
and I did it, using some "conduit" inside Calibre. I sent all my books (and later my music scores) on a tree like Books/<author-name>/<file-name>, but you can do it more complicated, using book-serie for example.
You must first start Calibre then connect your Poke or Max to the PC, then a new menu entry appears (Preferences and/or Peripheral ?) where you can customise where you want to put your files and with wich tree structure. Caution, Calibre scans the Poke for books already on it : it may take time ...
In Preferences / Share, click on "send books to peripherals", then adapt ! I put "{author_sort[0]}/{authors}/{title}" for the books and removed the first part for the scores.
In the bar, another button appeared : "Peripheral", there you can customise the name of the file ("{title} - {authors}" for me) and where you want to put all the structure : remove the list and enter the head directory.
Good luck, (it's not very easy the first time(s))
Denis