You have to drag the books down to the application area where you will see Bluefire. The standard itunes book sync is only for iBooks, and does not share a data store with other book applications (bluefire, stanza, amazon, etc).
I prefer to use the bluefirereader://nav/transfer method because I hate iTunes with a passion (I sync my iPhone with it only when I need to upgrade the OS). Until Bluefire gets generic OPDS catalog support, //nav/transfer is the only way I put books in it.
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