We are in process of remodeling and expanding our 1200 sq ft house. We will be adding 1272 additional sq feet. We currently have central heat & air. The furnace does not need to be replaced as it will heat up to 2500 sq ft. The air conditoner is a different story.
Two companies have come out. If I zone the house with two programmable thermostats I can turn my house into a zonal system and be able to keep my current a/c unit. The other wanted to wanted to put in a new a/c and thermostat. Does anyone have central heating system with two thermostats and if so how well does it work? Or, should I stick with the traditional system? Thanks.

One thing you may want to think about is how old is your current A/C? If it is more that 10 years old, you may be better off replacing it. Another thing is the calculations on A/C size involve estimates. How well insulated and sealed is the house, how much shade, activities in the house, long steamy showers, etc. How much of the time does the current system run on the hottest days? If it is not too much, it could be adequate. If you zone, you are going to have to have dampers or a separate air handler. Maybe skip the second system and put in a larger one later if you find you need it. Watch code.

Our AC is 4 yrs old and is 2 ton. We should get another 4-5 yrs from it and at that point we would replace the AC and furnace (10 years now). We are going to replace all the windows in the house and insulate all the old walls. I think because of how the house will be changing, it have new duct work. I like the idea of regulating the temperature throughout the house. I think our biggest concern is what happens on those days (hot or cold) that we occupy both zones of the house. The way the house is designed is the bedrooms will be one zone and the living, dining, kitchen, office, etc will be another. The bedroom zone will be approx 900 and 1700 for the rest. It is mainly in the evenings and weekends that we occupy both regions.
Can you tell somewhere I would be able to learn more about zonal systems? I am having a hard time finding information that combines central heat and air and zoned systems. Thanks.

I can't help too much. For zoned forced air heat or A/C, you need separate air handlers or dampers in addition to thermostats. There are a few past questions here with some information. Most zoned systems are hot water heat with each thermostat controlling a zone valve and linked to the boiler and pump.