When you insert the card, the device searches it for books and processes them into library. The library list should show them. There is no indication whether the books are in the main memory or the SD card.
The books can be put anywhere on the card so long as they aren't in a folder starting with a dot.
If the device info page of the settings shows the card is there, the books should have been processed. But, if there is a problem with one or more of the books that means they can't be processed. When that happens, none in the current batch will be added to the library. Unfortunately, there is no indication of which book caused the problem. You will need to remove all the books and add them in smaller batches until you work out which is at fault.
What I would suggest is to remove all the books from the card. Then add one that you know works. It can be the same as one on the main memory as the device will see them as separate books that happen to have the same name. If you choose a book you have started reading, then the one on the card will show as unread.
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