The save template only controls the path and filename outside the library. You can't change the folders in the library. But after you have saved the book to the folder of your choice, using the save template, you can delete the book from the library.
The paths and names can be "constructed" from metadata like genre or published date or series whatever. Extremely powerful.
A typical work flow could be to add a set of books to an empty calibre library. Edit metadata and download cover and other metadata until the books are fine. Then convert and save the books. Verify that the books and the paths are OK. After that delete the books from the library. Done!
Of course you could also keep the books in the library as a backup or to quickly find out what books you already have. Perhaps even to search using tags or other features. Who knows, you might even skip saving the books outside calibre?
