I couldn't get the Arc to play nicely with Calibre, so my workaround is to use Dropbox or Sugarsync and to import EPub files from there. Once they are downloaded I import them to the library (via the menu in the top right) and it automatically finds anything that has been downloaded.
It's a good idea to click yes when the Arc asks you if you want to delete the downloaded file. This avoids duplicates and therefore pointless use of storage.
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