Apple approved the Eucalyptus 1.4 update yesterday, which allows Eucalyptus to use the full height of the new tall screens on the iPhone 5 and new iPod Touches. You should be able to get the update via the App Store now.
If you upgrade to an iPhone 5 from an earlier device then restore a backup of your old device to it, or if you upgrade from an earlier version of Eucalyptus that's already on your iPhone 5, Eucalyptus 1.4 will re-lay-out the books to fit on the new, taller screen. I've worked hard to ensure this process works well. As always though, please email firstname.lastname@example.org if you have any problems after the update.