Forget: Save to Disk, Save to Folder or Send to device. These are all for EXPORTING the contents of the Library..
Basic Rules to prevent corruption:
1)make no changes to any filename/folder found in the Library as this will damage the Library data.
2)allow Calibre and plugins to do just about everything else
95.5% of the time, a typical user need not ever look inside the Library folder.
Adding books is simple:
1) Set your Add Books Preferences (Preferences: Adding Books) to reflect the way your book collection works. You will need to craft an appropriate inport REGEX if your method uses the filename.
Note: Import only can use filename and NOT any other part of the PATH
If you are doing a lot of books, I would NOT suggest enabling conversion to default output format (at this time)
2) right click the add books Icon and select the best choice for your book collection. (you indicate at least 2 paths. That will be 2 Add sessions)
Be prepared to wait. The time depends on how many books are in the path