IF you really were on B&N 1.1, then the original autonooter 2.12.25 WON'T work properly. However, there is a version of 2.12.25 that has been modified to root B&N 1.1. (it was put out in the "wild" and not given a newer version number. Laster version 3.0 of autonooter was released; but I don't think it was any different from the modified 2.12.25).
The best thing to do is try and see if you really are rooted (check for the Market, Youtube, Gmail etc). If you are, then I wouldn't change anything.
If you notice problems, then you can try autonooter 3; or you can take the 2 step -reset dance (8x reboot + wipe memory in settings); and then get your NookColor updated 1.1 and then use autonooter 3.