You don't (can't) control the structure of a Calibre Library.
If that is a 'must', then Calibre is NOT for you.
You don't get to tell your public library, how to file books. Well Calibre is the Library.
Calibre files books:
Author
Title (ID)
Formats
Cover
(backup metadata) OPF
You can use the Tag browser (Think of that as the 'Card Catalog' from days of olde ) to search and select, The Send to device, save to disk or Save to folder; to get the to your EXTERNAL reading device