We don't know for sure yet.
It is almost certain iBooks will support reading unencrypted ePub files, however, and that means managing those through iTunes. If third party apps which read unencrypted ePub files are allowed on, we'll have have to wait and see.
There's mixed data about how easy general file transfer to the iPad will be, you may need to use the same stupid trick of an app with a web server built in as for the iPhone.
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