There will always be temperature differences even from one side of the house to the other. I live in a single story home and installed a 4 zone set up before I moved in here 6 or so months ago I've seen temperature differences of 10 degrees from one side of the house to the other.

Obviously those without zoning could only guess as to what the difference is in their home... unless of course they happen to put a thermostat in those areas.

In a two story home you fight a fight that can be even worse, because the natural flow of heat is that it rises to the top of the ceiling however high that goes.

The cause of this problem is associated with a few different things and each of these things can have an effect on the problem to 'one degree' or another.

The room(s) that are hotter have no control to operate the HVAC system. If these room(s) do have the control to operate the HVAC system other areas of the home are probably too cool in order to make these hotter room(s) comfortable.

There may not be enough air flow to these room(s) to adequately control the load being placed on the room(s).

They may not be insulated properly. I know this sounds stupid, but you'd be surprised how many times in a given year I see poorly and even NO insulation on the opposite side of a 140 degree attic that the attic even suffers from poor ventilation among other serious problems.

How does the sun fall on these areas? Typically the west sun will pose many challenges on temperature control within the home.

There are more and more homes that have HVAC zoning from one degree to another. The problem is that many times the approach is completely wrong and in some cases the approach is not adequately used to address problem areas with in the home.

An air conditioner will only do the best it can when it is designed to handle areas of the home like this. You could easily have rooms within the 2 zone set up that are 5 or more degrees apart. If you lack control of the system the system doesn't know that it's 5, 10, 12 degrees hotter 15 feet from the control that is with in that zone.

It would be like having 3 rooms on first floor, 3 rooms on second floor with 2 light switches. Your complaint would then be my light bill is too high why can't I shut the lights off in the rooms I am not using?

With that said, zoning is complicated because of sizing. Single speed systems can easily be zoned and will work better than a single speed non-zoned system. However, due to sizing it complicates things. I often say zoning isn't for everyone nor every house. It is a 'hands on' type thing that should only be discussed in person with a pro at your house. A 2 speed or more HVAC system is a much better candidate for zoning... but costs to do it properly are prohibitive for most.

Without that, you're likely to be faced with what you have now or what you suspect you will be faced with given your limited knowledge of the situation.

For more information with video on this subject: 2 Story HVAC zoning information