From your description above, I think that you didn't use CC to connect to the content server but instead used the Fire's web browser or ES itself. Is this correct? Assuming I have it right ...
CC cannot "see" books that it didn't obtain itself, either using its wireless device connection or its content server connection. In addition, CC cannot "see" books that are not in the folders supplied in CC's settings. And CC cannot "see" books sent over a USB connection. The "right" way to do what you just did would be to use CC to connect to calibre's content server and download the books there. Alternatively, connect as a wireless device and send the books.
If all you want in CC is the metadata then this thread might be of interest:
https://www.mobileread.com/forums/sho...d.php?t=251653
If you move the books from the ES documents folder to a CC folder, or alternatively tell CC that it should store books in the ES documents folder, then the next time you connect as a wireless device CC and calibre will attempt to match those books with the calibre library. This works rather well for epubs, but does not work well for PDFs.