I'm leaving my 2 piece. Seems to sit a little higher. But it does suck having to pay 130 bucks for a new center bearring!!! 
Plus I'm to lazy to build another shaft!!! 
There should be no difference in height between a one and two piece shaft. That is, if the two piece shaft is setup correctly. The two piece shaft with carrier bearing is designed to be in a straight line, meaning no angles at the carrier bearing. When you lift the truck, it induces an angle at the carrier, which leads to vibrations and damaging the carrier. So, if your one piece shaft is a straight line, and your two piece is installed correctly and is also in a stright line, there should be no height differences between the two.
To correct the angle at the carrier, try shimming the carrier down further.
