It looks like you can set two paths in your defaults.persistent.lua:
https://github.com/koreader/koreader....lua#L220-L226
Code:
-- Set a path to a folder that is filled by Calibre (must contain the file metadata.calibre)
-- e.g.
-- "/mnt/sd/.hidden" for Kobo with files in ".hidden" on the SD card
-- "/mnt/onboard/MyPath" for Kobo with files in "MyPath" on the device itself
-- "/mnt/us/documents/" for Kindle files in folder "documents"
SEARCH_LIBRARY_PATH = ""
SEARCH_LIBRARY_PATH2 = ""