In order to read eBooks.com titles on your Nook, you will need to purchase books in ePub or PDF formats.
Once purchased, in your ebooks.com account you should see a download link.
This should take you to a page with 2 steps, firstly to download Adobe Digital Editions and the second to download the ebook.
Go to Adobe and download, install and authorize Adobe Digital Editions 1.5 if it is not already on your system.
Once you have your books downloaded, you can then open Adobe Digital Editions and connect your Nook. to transfer files.
Adobe Digital Editions should recognize your Nook and show it as a new bookshelf for you to transfer from within Adobe Digital Editions.