Here is an excellent and easy-to-follow guide on how to automate adding your books to Calibre:
http://dearauthor.com/ebooks/using-b...es-to-calibre/
This particular guide is for Windows. There should be a link in the article for how to accomplish the same on a Mac.
I found it to work seamlessly once set up and it should eliminate any confusion as to what has/not been added to Calibre already.