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I would put applications and their data on the same card. That way, if you have to remove the card for some reason, the app and data goes together. You don't have idle data taking up space with no app to access it, or an app with no data. Put optional stuff on the CF card, as it is more likely to be removed. Put the "keepers" on the SD card, leave it in the slot most, if not all, of the time. I put the really nice to have stuff in Built-In Storage so that it's with me even if the cards are both out.
Of course, it is really up to you. You will have lots of flexibility.
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