It is no problem to use the Nook with ADE. I personaly prefer Calibre. You can send all your DRM epub books via Calibre on your Nook.
But you know, that you cannot send your Amazon books on the Nook. It cannot read that format. But if you "free" them, you can convert them to epub and send them on your Nook either.
But I have to tell you one thing. At the moment there is no way, to organize your personal library on the Nook. Only the B&N stuff can be organized by auther, date or title.
The software update is actualy expected today, at least, that's what the say at the B&N forum. Maybe after that, it will be possible to organize side loaded stuff too.