You would be better off with two separate systems.

I would want a two stage var speed furnace. Post mdl of furnace and the thermostat/control.

If the basement is below or partially below grade, heating and cooling BTU requirement should be low especially if basement is insulated good. In floor heat is nice but probably pricey. I think you have to take that into consideration along with how you see the basement to be used.

Zoning controls are nice if dealer has demonstrated and verified experience in this area. This is not a job for a novice. Correct sizing and ductwork design is a must. Carrier Infinity controls are generally regarded as the best in the residential marketplace.

IMO

What do you mean about the two systems? I would think that is going to cost too much.

I am mostly sold on the two stage upgrade, but the $900 increase in cost seems a bit much. Originally we had the 58HDX Comfort 95 from Carrier in the bid. I do not know the details on the upgrade unit besides it being a 100k BTU 2 stage with ECM. If we went with 80k it would cost $100 less.

The in floor heat for the basement is a huge expense. The rough-in is $2,700 with another $6,500 to finish it off. I will more then likely pass on this option.

I am interested in multizone, but was wondering if you can get the same results closing registers throughout the seasons.

Closing registers is never a good idea. You want damper controls on the supply line for each zone especially if you don't plan to install zoning controls.

And make no mistake, you get better comfort and control with two systems over one.

Keep the registers open.

IMO

My first suggestion is for you to speak directly to the HVAC contractor. From what you have written the builder does not seem knowledgeable about HVAC systems. The installation of the HVAC system is critical. You want to be confident the HVAC contractor is reputable and knows what he is doing.

My vote would also be to install two systems. Yes it is more expensive, but you will have even temperature distribution. The alternative is multiple zones. This requires an HVAC contractor who is experienced in zoning.

You don't need to spend the money on the basement rough in. It doesn't take much to heat an insulated finished basement.

I just got some info from my builder that said the cost for each zone is $1200. This include auto dampers that are not thermostat controlled. Does that cost seem fair?

Auto dampers that are not thermostat controlled?

Code in NC requires 2 systems. Common sense requires 2 systems. Zoning is an alternative that saves very little money because good zoning costs money.

Closing registers is okay if you have all ducts in conditioned space (or at least basement) and you have oversized your duct system to never create a high pressure system. But oversize ducts can be a problem.

If you have a single system, where is the t-stat. Downstairs? Bedrooms upstairs? Then on a really cold night, you have to guess what temp downstairs will make you comfortable upstairs. Usually, there are far more windows downstairs and that area loses heat faster (in a new house) and so a particularly cold night will make upstairs warmer than you want.

The concept of one system on a new house in 2012 in a severe climate is absolutely shocking to me. Apparently the NC code agrees with me and we are mild compared to you.