My boox also works great with calibre and series. The way I have it set up is that each author has a folder. If there is a series calibre creates a subfolder within the author's folder with the series name. Inside the books are listed with the series number and title. Non series books are listed directly in the author's folder.
Also check into
calibre2opds here on mobileread. I creates a catalogue of your calibre library in either opds or html format. Calibre + calibre2opds + dropbox + stanza = my favorite combination for reading on iphone.