I had a similar issue when booting from CyanogenMod 7 off my 16 Gb SD Card - and I tried Easus Partition Manager but the instructions over on XDA are sketchy at best.
Best method I've found is via WiFi File Explorer (in market). It allows you to upload files over WiFi either to your SD Card (as well as make new directories, etc) or to the Nook Color internal emmc - give it a try (must be rooted).
You can also transfer files to the internal emmc [there's about 5 Gb free) via USB but it's painfully slow.
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