An alternative method
Calibre Companion is great (just got it myself), but before I found the app I was using the "Connect To Folder" option under the Connect and Share tab on Calibre. I created a folder titled "Temp Ebooks" (you can name it whatever you want) in "My Documents" in Windows 7 and then sent whatever books I wanted on my device to that folder. I then copied and pasted the folder onto my Nexus 7 internal SD. Worked like a charm, and all the books were in folders by author.
Just another option if you want.