Dear Author has a great tutorial for Calibre users. Here’s a snippet:
Intro
Now that you have your Calibre database set up just the way you like it, you need to figure out how to get the books from your computer to your device. You can use the tethered or the over the air (untethered) method.
Tethered
Tethered means to physically attach your device to your computer using the USB cord. Calibre recognizes almost every mainstream device from the Kobo, Sony, nook, Kindle, Cybook, and the iOS devices.
Send to Device
Once you plugin the device, you should see a “Send to Device” icon on the menu bar.
Also covered are various untethered methods of transferring ebooks.