Just follow the steps in "NookDevs" they are very detailed and exact.
The link is NookColor Rooting
They tell you how to upgrade if you have FW 1.0.0 or 1.0.1. I had 1.0.0 but I chose to upgrade first.
Also I do prefer the "auto nooter" tool. They configure and install some key apps and if your scared you might want to go this route since it will calm you nevers a little knowing somebody has already gone through the pains of preconfiguring a nook.
If your like to know the whole process it would be best to do it yourself.