When I connect my iPad to my iMac, and open
Calibre,
Calibre does recognize my iPad and will load books onto it. No special settings required.
What you seem to be suggesting, copying books from your iPad into your
Calibre library directly, is a little backwards. Download the books to your PC/Mac, put them in
Calibre, then transfer them to the iPad. If the books you have are from iBooks, I'm not sure how that would work, but from any other source this is the best way to get your books into
Calibre.