I am also the stoker of a tandem team, and I, too, have noticed that my riding position is different than on my single.
Our tandem came stock with a suspension seat post for the stoker. The reason is that on a tandem, road buzz, rattles and jounces are amplified by the time they reach the stoker. I was skeptical, but after some saddle time, I think it does help.
The stock saddle, however, was thrown out immediately. It was too wide and too soft. I put a nice, flat, hard Specialized Women's Pro saddle on, and that eliminated the butt soreness and numbness I was experiencing.
Finally, I found that since I tended to be out on the tandem longer (more miles), my older and cheaper cycle shorts didn't cut it. I invested in a pair of Pearl Izumi's, and they took care of the rest of the minor discomfort I was experiencing.
It is not the destination, but the journey...