Air bags do not distribute weight. They merely change the angle of the body. Either adjust the weight distribution (WD) with no air in the bags. Or head to a scale and get the axle weights before and after the WD is engaged. Once your axle weights are set then you can use the air bags to adjust the attitude of the body and make it look level.
As far as the differences in the ride heights there are many different factors that come into play. You could have one spring that is a little weaker than the other . Many trucks have the fuel tank on one side of the frame only. Do you have a tool box in the back with something heavy on one side?