If you rooted your NC, as in used the Manual Nooter process to gain root access, then you would still have the B&N UI, as well as the ability to install apps. It sounds like you may have replaced the B&N operating system with a custom ROM.
What did you actually do? What instructions did you follow?
Most likely what you need to do is revert to stock, update to 1.2 (if that's not your stock ROM already), and use Manual Nooter to gain root access. You'll find all of the above in XDA's Nook Color Development forum:
http://forum.xda-developers.com/forumdisplay.php?f=864