[Ken Maltby]

With the Kobo "drivers" in calibre disabled, and using the "Send to folder" function aimed at your .Books folder, calibre should have no problem seeing the folders it will add to .Books and the metadata catalog it creates there.

Using other "Send to device" methods, the metadata catalog and the folders caliber creates will be added to the root of the device (/mnt/onboard and /mnt/sd). Koreader allows you to set two locations where it will look for the metadata catalog.

Luck;
Ken