That's another user with similar question (few posts above yours)
And using CWM is really easy ... just read it few more time carefully. The changed kernel for multitouch & USB doesn't care what kind of way you used for rooting the Nook. CWM is a tool how to get the file inside the ZIP where you need it.
In yours and mine language ... it changes the files while the system if OFF. That's good because if the system would be running, it would use those files and if you would change them while being in use - it could confuse the system = mess = restoring your nook again.
CWM will just do the job instead of you. You just burn it on the SDcard, start the Nook with the card in it ... then you will just choose which ZIP file you want to use & that's it.