The initial syncing has to be brute force as Kovid and @theducks said. After that, there are other methods.
My method is with the Reading List plugin. I create a reading list for each device. When I get a new book, I add it to the lists of the devices I want the book on. When I connect the device, I sync the list (which can be automatic), the books are sent and the list is cleared.
Also, as both devices are Kobo devices, you can also sync the reading status. My Kobo Utilities plugin has function to store the reading status in calibre when you connect the device. You can restore this to the other device. It isn't all automatic and you can usually just turn the page a few times to catch up on the other device, so it might not be worthwhile doing this. I mainly use it when I finish a book to mark the books on the other devices as read.
|