To unroot your nook color you can follow this guide up here in XDA, I have looked it up for you. There is no simpler way to do it, there is a 3 finger wipe you can use to restore you nook back to stock if you want a manual way, but it takes precision on timing and waiting for an eighth reboot attempt on the nook color. http://forum.xda-developers.com/showthread.php?t=931720
I give instuctions on how to do this in the nook color cyanogenMod threads here, this link provides the simpliest method that I know of along with youtube videos and all of the download instructions to get a microSD card working with cyanogenMod on it. The link to this forum is here. http://forum.cyanogenmod.com/topic/55338-new-to-nook/
The hardware button wipe to restore your nook color to stock can be found here up in XDA's nook color forums here, some people perfer this method instead of using a recovery image on a boot card to do so. http://forum.xda-developers.com/archive/index.php/t-1461172.html
If you need any further help on rooting the nook color, putting cyanogenmod on the card feel free to leave me a thread on further help up at cyanogenmod. com nook colors forum here. http://forum.cyanogenmod.com/forum/225-nook-color-general/
Some of the instructions to go over rooting the nook color can also be found on cyanogenMods own wiki here also for you to look at. http://wiki.cyanogenmod.com/wiki/Barnes_%26_Noble_Nook_Color:_Full_Update_Guide
As you can see there are other avalible sites listed with guides for rooting your nook color with cyanogenmod on it and/or reverting your nook color back to stock. Feel free to leave me any questions on doing so up at the cyanogenmod forums.
Since you liked Autonooter, you will like ManualNooter 5.2.19 which is found here.
My NC is dual boot from emmc with BN/MN on the alternate partitions and CM 7.2 on the primary partition. This way they both share the same uSD card data. Those instructions are here.
In either case, it seems that B&N 1.4.3 update takes a while to install, even after the NC becomes usable. Also, download your B&N stuff before applying MN. Maybe some indexing and conversion stuff is still happening in the background. So be patient on the B&N upgrade to 1.4.3 before appying MN. As for the MN install, Market/Playstore is finicky at times, and it seems that patience is required for it to install its own updates before Market/Playstore really works.
I would also recommend applying Dalingring's OC Kernel to MN. It is found here, which this link supplies apps2sd support.
Enjoy the update!
Start by installing Titanium and backing things up, then follow the wipe and root guide of your choice.
One note of caution - the cyanogen mod guide I just skimmed makes the assumption that you want to install Clockwork Mod. Installing CM and/or a new kernel (the overclock kernels - which I also like and do use) means that your device is very far from stock and recovery using the standard methods may not work.
My guide to wiping, installing a clean Nook OS (written for 1.2 but applies to 1.3 if you use the flashable file Taosoar located,) rooting it and blocking updates is up at
but, I discovered this summer that the 1.4.3 update will apply itself unbidden even if you are running an alternate kernel.
This disappointed me; for many iterations of the OTA update, the overclock kernel I was running made the OTA update fail.
At this point, I'm not paying so much attention to the OTA and am instead just ready to re-root. The rooting tool I threw together for the Simple Touch and Glow works with very few changes for the NC as well, so long as you don't need the Market - I'm able to do without because I reinstall Titanium from the command line, followed by a reinstall of the apps I want. Since the Amazon marketplace is so much simpler to have running than the Android market is, I simply use that.