First, I also support JKenP's recommendation to start with the basics. Calibre really does have a gentle learning curve and this forum makes it even easier.
A couple of points:
Books you purchase from B&N will download when you turn on the wifi. Very easy. Also, you can sideload books you've acquired elsewhere (highly recommend Calibre for this). Sideloading- with or without Calibre- does not require rooting. You can sideload books right out of the box. Sideloading is for non-B&N purchased books.
The good news is that regardless of how the book got onto the device, all books (B&N and sideloaded) appear in the same library. Think of the library as one giant shelf with every book on the device listed there. From the library, you can select a book and start reading it. The Nook will let you view by Author, Title, or Most Recent. It will also search for Title or Author if you have a lot of books using an onscreen keyboard.
The catalog I referred to is a capability within Calibre. Calibre can, at your direction, create a new ebook with information you choose about the books in your Calibre library. You can then load that ebook (the catalog itself) onto the device and flip through the book as a semi-workaround for the lack of collections in the Nook interface.
I used Calibre for some time before stumbling onto the catalog capability. Again- start with Calibre's online documentation and come back with questions!
Last edited by MooseFam5; 01-04-2013 at 11:12 PM.