The latest release of calibre (0.7.2) includes a significantly improved iPad driver. I've revised the overview in the first post in this thread
describing the implementation.
The most significant change is that the driver now supports either manual or automatic syncing, and iTunes-managed storage or self-managed storage. This means that you don't need to keep an extra copy of the uploaded epub in iTunes.
Please review the initial post in this thread
to understand the implications of these changes.