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Apple do not allow third party programs to transfer books over USB in the current iPhone OS releases. That is why you will find that all the current eBook apps use Wireless transfer.
This restriction is partly lifted on OS3.2 (as used on the iPad) and will also apply to OS4 when it is ready for the iPhone. With those releases the 0.7 version of Calibre will be able to interact directly across the USB link with iBooks and with Stanza making transfers much easier for those without WiFi links.
Having said that, once you get the wireless link working it is much more convenient than using iTunes as it can also be used over 3G (i.e. when you are away from home). This means you can download ebooks when you want them rather than having to pre-load them all in advance.
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