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Thanks for asking.
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Regarding your question:
I have never used Prezi before, but just had a quick look. As far as I can see, you can control Prezi presentations with the left and right cursor keys. If that's all you need, what you'd need to do once your Prezi presentation is on screen is this:
1) Access the Remote Buddy menu with your Apple Remote and select the Virtual Keyboard Behaviour (to be found in Virtual Input Devices or System > Virtual Input Devices).
2) If the onscreen keyboard shows up now, you can dismiss it by pressing the Menu button.
3) If no onscreen keyboard is shown (or not any longer after 2), the Virtual Keyboard Behaviour's default mapping maps your "left" and "right" buttons to emulate left and right cursor keys. Which, if my observations are correct, should be all you need to control your Prezi presentation.
Best regards,
Felix Schwarz