It looks like it will work. I just tried it out using Google Docs, my PC, and the Nook. I uploaded an epub into Google Docs. Then I went into Google Docs on the Nook with FileManager and copied the file into the clipboard (you use the clipboard for file copying). Then I switched over to the books folder on the SD card and did a paste. The epub was there. I then looked in the Library on the Nook and that epub was listed in the books area.
So you could use Calibre the same way (instead of Google docs - I was too lazy to hook up the Nook to my PC).