What are the recommended settings for a dual-zone air conditioning unit?
A simple solution is just to set the thermostats up with an allowance between them to compensate for the thermal convection. This allowance is usually around two degrees, depending on ceiling heights on each floor.

For example, if your preferred temperature in the Summer is 74&deg;F, set the downstairs thermostat to 73&deg;F, and the upstairs to 75&deg;F, in effect bracketing your desired set point. The same two degree difference will usually be sufficient in the Winter as well. Just remember to always have the higher temperature on the higher floor.

For three story homes, a one degree difference between each floor may be sufficient, depending on how high the ceilings of each floor are. Just as with the two story home, the highest temperature always goes on the highest floor, no matter what the season.