That's a good question. If you are running rooted stock, then you might as well install cwr to eMMC. Download Rom manager, run it and select the "Flash clockworkMod Recovery" option, then just select "Reboot into Recovery". Then have the kernel you need (make sure you get the eclair kernel if running stock) on the sdcard and select install from zip, and choose zip. Reboot and run setcpu.
I'm fairly new to this as well, but I spend most of my time reading these forums, yeah I'm boring like that, just ask my wife.
Edit: Oh, if it asks what device, select Nook Color. Do not select the (old) option. I think it asks that.