Depending on the size or the layout of the house, you might want to consider two central systems – usually one for the upstairs and another one for the main floor. This way, you can adjust the temperature up or down in those areas independently and reduce your overall energy consumption.
For the areas where people will be sleeping at night, I would also consider a central system with some sort of capacity modulation – either one with two steps of capacity or continuous capacity control along with a variable speed or stepped indoor air handler. This will be especially important in warmer and more humid climates because of the comfort and health problems associated with humidity control are almost as important as the temperature control in those climates.
If you choose a capacity controlled system, usually 16 SEER or greater, the system will be able to adjust to the load on humid nights when you need the system to run at low capacity for an extended period of time. This will ensure that the humidity is removed and the air remains fresh and filtered. The same system can still run at the full load capacity during the day when the demand for cooling is most critical, or vice versa depending on the climate you live in. The other benefit of these systems is that they run very quietly at the low capacity mode.
You might also want to consider also adding a remote ductless mini-split system If you have rooms in your new home that are in remote areas and are located far away from the central AC system – e.g. an attic space or “bonus” room . These rooms are frequently zoned off from the rest of the house or used only occasionally. A ductless mini-split is a type of air conditioning system that does not use ducts to transfer cool air, and instead the outdoor condenser unit is connected directly to an interior air handler. Because of this direct connection, generally only one room or space can be cooled at a time making ductless mini-splits a viable option for room additions or add-ons.
Investing in a new, custom built home involves a lot of decisions and unfortunately the HVAC decisions are sometimes overlooked. It’s always best to consider the comfort and energy cost factors as well as the many other decisions you will be making. You might also want to consider talking directly with an HVAC contractor instead of relying entirely on the general contractor to know the latest about HVAC technology and options. Good luck with your new home!