I am a bit confused when you talk about managing your library within your
Nook. What I think you started out talking about was trying to see the
Nook on the Library View bookshelf when ADE is open, so let me deal with
that first. It's usually just a matter of sequencing.
You should attach your Nook to your computer first, and wait for the
computer to assign it a drive letter. When that's done, then you can bring
up ADE which should see the Nook automagically.
When you're done, you want to close ADE first and wait until the Nook tells
you it's finished processing its new content. Then, you need to eject the
Nook from your computer, so your operating system detaches it logically.
In Windows, you can do that from the START taskbar: the extreme right hand
corner and the icon that looks like a small calculator.
Hope this helps!