I don't really feel qualified to help you with this as I have had very little experience with Calibre. I do know that you need to have the reader attached to your computer via the USB cable so Calibre can recognize that it is present before you can download your reformatted eBook/document to the Kindle (you probably already had this figured out....
)
There is an entire forum here on MobileRead devoted to Calibre with a lot of knowledgeable and helpful people there; post your questions about the program there and you will get assistance:
Calibre
Holly