syncing is never going to happen. The number of possible problems with that are legion.
You can add books from your device to calibre by right clicking on them and selecting add to library (or dragging and dropping them onto the calibre icon in the toolbar).
Since the Nook exposes no metadata database for manipulation via the USB connection, metadata updates have no way of being propagated to the device except by resending the books. If you want automatic metadata propagation get a SONY.
The best workflow I'd suggest for you is:
right click on the books, to add them to calibre, then delete from device. Then re-send using calibre.
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