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iBooks supports iTunes sharing, and it's pretty easy to copy books to and from your iPad by connecting your iPad to your computer's USB port and sharing the file via iTunes. But it's kind of annoying to have to connect your iPad to your computer every time you download an ePub file. Here are a few additional methods for getting ePub files on your iPad.
iBooks also supports the Open In... feature, so you can email yourself an ePub as an attachment. Tap the attachment in Mail on your iPad, and you'll be asked if you'd like to open the ePub in iBooks (or any other app on your iPad that can read ePub files—for instance, Stanza). You can also tap a link to a .epub file in Safari on your iPad and use Open In ... to open the ePub file in iBooks (or another app).
But an even easier way to move an ePub from your computer to your iPad is to use DropBox. You can get a free account at DropBox.com with 2 gigabytes of storage. You can access that storage on Mac OSX, Windows, your iPad, and even on an iPhone. That means you can easily share files between your devices and with others, publicly or privately.
To transfer an ePub file to your iPad via DropBox, first copy the ePub file to DropBox, and then use DropBox to send the ePub to iBooks. Tap the ePub file in DropBox on your iPad, then, in Portrait orientation, tap the Action icon (the curved arrow inside a box) at the top right of the DropBox window. You'll see a pop-over menu asking you what application you'd like to send the ePub file to; you can choose iBooks or Stanza or any other ePub friendly app installed on your iPad.