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I tried to root mine and failed. The installer partitioned the card, and Windows could only see the OS partition. It is not obvious how to undo this. However, when I plugged the card in to the nook while it was on, it identified it as an SD card, and asked if I wanted to format it. I said yes, and it redid the partition as a single partition for the full size of the card. So I'd say the answer is no, you don't need two cards.
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