CyanogenMod 10.1 can be installed easily to the EMMC on a Nook Color. When an updated ROM of CyanogenMod 10.1 is released, it is pretty easy to update your Nook Color to it.
Download the new version of CyanogenMod for Nook Color from here. It is a zip file. Copy the zip file to any micro-SD card that can be read on the Nook Color.
Power off your Nook Color. Insert the micro-SD card into it.
Power on the Nook Color. When you see the CyanoBoot bootloader screen, press the Nook (N) button to get into the boot menu. Choose Internal EMMC Recovery. This boots your Nook Color into ClockworkMod.
In ClockworkMod, first choose Wipe cache partition.
Next, choose Install ZIP file and choose the CyanogenMod ROM zip file you copied over. It takes a while to install it.
Once the install is done, choose to reboot. You will reboot into your updated CyanogenMod :)
Tried with: CyanogenMod 10.1 (Stable) and Nook Color 8GB