Simply connect to the root of the SD card. All books will be placed onto the root of the SD card.
The device template can be customized with a metadata save pattern, which by default puts all books into author folders anyway. You can set this by clicking the arrow next to the device, and selecting Configure this device (see screenshot).
The "Save template" can be changed to store books in the root of the SD card. For more on how to use templates, see Preferences ==> Sending books to devices
Or take a look at the
official guide.