There's no need to use sync to transfer epubs to the iPad. You can drag them into the iPad's book list and they get transferred over in a couple of seconds.The only thing is that it didn't work for me. This morning I once again attempted to recreate his steps, and I dragged over the ebook to iTunes, but it wouldn't accept it. The list was all grayed out. And I was just about to write just that, when I thought about why it was grayed out. And I realized it was because I have iTunes set up to automatically sync.
All I have to do to get more granular control is select the iPad in the Devices list and then in the Summary tab, check the Manually manage music and videos option.
Now I can drag individual files—like ebooks—to the iPad and they are synced almost immediately. This will save me a lot of time.