IMHO the overview part of this is the issue.
Physical Libraries can be on any (full access) local drive
As to Moving Files:
Select Books: Right-click: Copy to Library:<name> (optional delete after copy)
The Selection process gets tricky.
Basic Q Do you want to move ANY book (all formats) that HAS a PDF?
I used a custom column to track Master (source) formats as a tool against future conversions, wher I want to use the Original as the source.
If you have only PDF, piece of cake (chocolate

) ; Use the Tag Browser to select PDF in the custom col or
search: formats:PDF and Not formats:EPUB
The goal is to get only the books that exist solely as a PDF
I believe Betteread has large libraries