To flash anything you need to make a bootable CWM SD per my instructions in my HD/HD+ CWM thread. You cannot flash things with stock recovery. Once you have made the CWM SD it is just as easy to flash the Universal Root rev3 zip and enable unknown sources zip as it is to flash the stock 2.1.1 rooted zip. Even with the full rooted version you still need to flash the enable unknown sources zip. And you end up exactly the same no matter which way you go.
All of the zips get flashed the same way with CWM, including the full stock zips and custom recovery for internal memory.
Sent from my Nook HD+ running CM10.1 on emmc.
See my Nook Color Tips Thread here
and my Nook Color EMMC Partition Repair Thread here
and my Nook Color Updated CM SD Installation Instructions here
and my Nook HD/HD+ stock tips thread here
and my Nook HD/HD+ CWM Root Tools thread here