With the recent addition of a robust content server interface there is no need to connect your device using CC and then go back to Calibre to push books, unless you've added hundreds of books to your calibre library.
Fire up CC on your device, connect to content server, and then select the books you want to download to your device.
There is also added functionality if you connect from CC as a wireless device.
If you haven't used CC for the last couple of weeks you should really fire it up and check out all the new stuff. Just make sure you upgrade both calibre and CC to their current incarnations.
Maybe one day Charles will take a break from adding even more magical features and turbo-boosting performance and will update the FAQ to reflect all the recent goodness:-)