1. Mark Folders as read.
Recently I've used 'clean slate' and now all my read books aren't marked as read any more.
It would be much simpler for everyone all around (even if the read books aren't in a separate folder before hand) to mark all the books in a single folder as read.
Even assuming you like to keep all your books in a single folder it'll be easier to move the read books to a single folder, at least this way you only need to move them individually once (back to your preferred location).
2. Multiple file select. figure out a key combination that will allow us to select more than one file/folder for file operations (move / delete / mark as read).