In my opinion, Having two separate units (especially if house is two or more stories) is preferable for reasons including:

1. Better control of temperature
2. Wear and tare of equipment (zoning can wreak havoc on coils if not controlled properly)
3. Less complexity of systems to go wrong
4. Ability to circulate air throughout different levels (zones) regardless of whether heating or cooling those zones is engaged (zoned single systems simply shut off duct to specific zone)

We also faced the same dilemna and live in SE Louisiana. We struggled with this same question last year when we were having a complete re-do of our HVAC. Previously,we had 2 systems....one up and one down. Since we were re-doing all our ducting and the way our house is set up....it would have been very easy to go to one top of the line zoned system. We came very close to doing that very thing.

Then...we kept going back to our 20 year experience of living with two systems. During the day..........the upstairs (bedrooms which are seldom used anymore....) is set at 83 degrees. Downstairs, where our master br is 77 during the day/74 at night. Our living area is kept quite quite comfortable. We have very good, middle of the road, 13 seer units, and our electric bill that just arrived yesterday (blinging hot last month) was $101. We are an all electric home except for gas hot water. Our house is always comfortable and NOT humid inside.

Several years ago, my husband had surgery and the day we came home...our 15 year old outside unit for the downstairs died. The upstairs unit was able to keep the house cool enough such that no one really sufferred until the new unit was obtained. Had we one unit....we would have been up the creek.

We do not have straight AC but rather heat pumps now with electric strip back up. THAT was a huge improvement going from straight AC!!!!!!!! Our electric bill in the winter was reduced by at least 40% for any given month and I didn't turn the thermostat down to where it was uncomfortable like we had to when we had just strip heating.

I think two good middle of the road units are better than on really fancy unit. We do have variable speed blowers and humidistat type thermostats. We are on the north shore.

We were lucky to find a contractor that really did a top notch installation.

Good luck.

my house has 2 HVAC systems. it is a 2400 sqft ranch style, so no upstairs.

one unit does the bed/bath areas of the house, the other does the rest.

shortly after we bought the house the squirrel cage died in teh unit for the bed rooms. we simply shut the hall doors, and slept on the hide-a-bed for a couple nights till the correct motor came in. they sent the wrong one at first, that caused a delay.

i sometimes wish i had gone with a single unit last year when we replaced the 30 yr old unit, but honestly i like the fact i can cool/heat only the area of the house we are in. both are off during the day, and at night after bed time the front unit shuts down as well. between the programmable stats and the new HP up front, we have cut our bill on avg 38-40% and peak months 50%! our recent electric bill was 330.00, 2 years ago it was 500, and the year before that when we had old manual tstats and 2 old units it was 650.00! same time period, comparable days.

Thank you all so much! We are a one story too. The consensus seems to be two units for practibility.
If I may ask another question, what type of ducting do you have, flex or rigid or combination? Both installers we have spoken to want to put in flexduct!
Thanks!

I like rigid metal trunklines (insulated) with flex connectors for ease of installation and noise attenuation. All-flex ductwork systems need to be done right for it to work well. That means strapping the ductwork, making it straight with no sharp bends, sizing it properly, etc.

Thanks Ryan, I appreciate the advice!

I think the zoned unit is a much better option. You'll save on your energy cost and its nice to have multiple thermostats. A zoned system recirculates air when some of the zones are not calling for heat or cool and makes the heat much hotter in the winter time. Feels alot like gas heat and whats great about that is it can get the heat without running the heat strips which is where your savings come from. My house is 2800 sq. feet in Arkansas and my average bill is about $150.00 a month. By far the best duct is hard pipe all the way to the boot/vent.