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You didn't say if your magazine was going to be ePub but asuming it is stuff like that doesn't get exported to ePub from inDesign. You would most likely have to hand code it yourself after exporting the main body to ePub. You will most probably limit your audience to only iPad owners if you succeed. Having a header move sounds like a big effort to me seeing as you cant even display an image in a table in iBooks, which is the iPad audience's main reader. There's nothing in Liz Castro's book about moving text. Just audio and video is about as fancy as it gets.
All of the fancy magazines I've seen for the iPad where stand alone apps.
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