[BetterRed]

As DoctorOhh has indicated the directory and file structures are not configurable

Nominally they are '/library/author/title/title - author.format'

Within the constraints of the host operating and file systems the usage of each level and names are user controlled.

My Journals library has what I think of as 'Journal Name' (Foreign Policy, Granta etc) in the Author column and what I think of as 'Issue Label' (Year-Month, Issue #, Folio Reference etc) as the Title. The fact that calibre labels them something different is, for me at least, a minor annoyance.

But I'm not sure how one would go about 'marrying' Calibre and Paperport

Writing a Paperport PlugIn for Calibre would probably need access to a Paperport API,
Writing a Calibre PlugIn for Paperport would require that Paperport supports plugins

Does Paperport have a published API and/or does it support plugins

BR