Unless you allow Nickel to run and import the books (plus a second connection to update the metadata), Nickel will not show the books. If you want to send books over WiFi or any way other than a bog standard USB connection, you can manually trigger an import using NickelMenu. Again, the books need to be in a directory accessible to Nickel.
Personally, I used Nickel 99% of the time with KOReader or Plato being started from NickelMenu for the few occasions that I am either testing or playing with a .pdf file so Nickel gets to run after a USB connection.
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