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Your iPad should synchronize through iTunes and probably doesn't appear on your desktop.
Two ways I have found to do this:
Using iBooks to read on the iPad
Using Stanza to read on the iPad
Easiest is iBooks and sync with iTunes.
Download iBooks and in the iTunes preferences/general make sure you have "Books" checkmarked.
On Calibre under the Connect/Share menu you can connect with iTunes and push books even when the iPad is not attached. But when it is attached it should recognize it as a device.
I figure you probably don't have iBooks and don't have your preferences set up for syncing books yet.
Try that and come back if it doesn't work or if you want to do the Stanza setup.
Archon
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