I used photoshop to stack and blend the 2-shot nadirs, before sending to PtGui. After PtGui, the panos where resized and sharpened in photoshop before going to Pano2QTVR.
Shameless plug for the NN3 (so I can get into the contest and win big. Although, I'm really very happy with the current NN3. Maybe one of those new rotators?) The NN3 is so small and light, that I was able to take it camping and hiking, and yet so accurate that I was able to template my first pano onto the following panos. Control points? With the NN3, the word is "easy". Let PtGui generate 'em, then go to the control point table, highlight anything over 0.55 and delete it.