The EMMC of the Nook Color has a partition for the ROM and a 5 GB partition that's mostly if not completely unused. Presently, there aren't any 3rd-party managers to move apps to that unused partition, so I modified the vold.fstab and am now able to use that partition for apps, files, etc.
NC.SWAP.VOLD.ZIP swaps the way the SD and EMMC directories are mounted. By swapping the mount points, and renaming EMMC to SDCARD, your apps, etc., will install to the internal storage, vs. installing to your SDCARD. Your physical SDcard is automatically mounted as "EMMC."
This also means that the music player still finds files, you can move files to "EMMC," and you can still eject the SDcard ("EMMC"), put it back in and it still shows up automatically. Now your NC won't freak out if you pull the card out without unmounting it - all of the apps are on the actual EMMC. You'd just find the SDcard under /mnt/emmc instead of /mnt/sdcard.
Because this ZIP file maps the change at an OS level, when you boot to recovery, your NC sees SD as the SDcard, so no issues occur. When you boot into your ROM, the mount points are swapped and you'll have access to the renamed "SDCARD" (5 GB) on your NC.
Use CWR 126.96.36.199 to install the .zip and check out the results with File Manager.
Thanks go out to Clark008, luciferii and Cali^Gal from #nookcolor, Loonacy and Raymondull from #Cyanogenmod, and EpicFail1236 from XDA.
Sorry if this is a bit crude, it's my first script ever. I would be happy to get any advice on how to make this better!
EDIT: I have been looking into renaming the emmc mount to say SD-External or better yet making it mount as /mnt/sdcard/sd-ext. it might be possible, ill be looking into it as soon as I can got laid up for a bit.