This may be a stupid question, for which I'll apologize right up front.

I live in Houston, and recently bought a 2-story home with separate upstairs and downstairs systems. The equipment is all fine (~9yr old Trane A/C & gas heat, inspected & maintained), but we're always either hot or cold because the two thermostats are hard to get set "right". This is partly because of the coarse temp scale and apparent wide deadband (?) that the existing t-stats (Honeywell mercury-switch types) have, but also because we have a large open atrium between the upstairs and downstairs, and both t-stats are located near it. So if the downstairs t-stat is set a little high when the heat is running, the upstairs t-stat stays warm and the upstairs heat doesn't come on... so the upstairs bedrooms stay cold. When the AC is running and the t-stats are a little "off", we have the opposite problem... cool upstairs, but hot in the downstairs living areas b/c the downstairs t-stat senses cooler air settling in the atrium, so the downstairs a/c doesn't run enough.

All this just means that it takes a little time (sometimes a few days) to get both t-stats set where they need to be. Then everything's great... unless we have to switch from heat to cool... in which case both t-stats have to be adjusted down, and it takes another day or two to get 'em right. From November to March, we're changing from heat to cool and back pretty often... sometimes several times a week... so it's rarely comfortable in the house.

Anyway, enough of the boring homeowner babble. I'd like to just put in a pair of programmable setback thermostats with auto heat/cool changeover - but I'm afraid that they might "work against each other"... upstairs cooling, downstairs heating, and both running all the time. So finally, my real questions:
- Is this something that's likely to be a problem?
- Are there any programmable t-stats out there that can control my two separate systems, but that will "talk" to each other so that they're either both on cool or both on heat?
- Is there some way to use a zone control unit to take the input from both thermostats, and have the it control the two systems "intelligently"?
- Or should I just forget about auto changeover?

Much thanks in advance.