Welcome to eReaders!
I don’t have a nook, so I can’t answer all your specific questions (maybe someone else can…)
But – you might be interested in a free program called Calibre to help you organize your eBooks. I use it with my Tablet and Kindle (and in theory the Kindle on my phone…)
It can convert (pretty well) books from one format to another (unless they have copy protection DRM on it….) So I can take a free Kindle book and convert it to an ePub book (or the other way.) It also will convert PDF’s. The Kindle can read PDF files directly as well (and some more complicated PDF’s don’t convert well with any software…) – I don’t know if the Nook can read PDF’s directly or not.
When I connect my Kindle or Tablet, Calibre will show me which of my many books are currently on the device, and I can tell it to copy it itself. I can also set up tags to help me find my books.
I can even setup other things (but it takes a lot of learning how) – Like I setup a category called “Curriculum” that is displayed at the side that is a folder struction. Under that I have AO, SCM, MA, etc… and then under those i have things like Year 1 or Module 1, etc. I can then just click into what I want to look at, and see the books I’ve assigned to those curriculums. (To do this wasn’t super-simple, but is in the Help files)
Anyway – just thought while you are going through the learning curve, you might want to add something else to learn…