You are looking at hot air furnace with AC system?

Nat gas will be fuel choice for heating?

You will get better overall comfort with two separate systems plus have a degree of redundancy if one system has a mechanical failure.

But certainly your home would be a good candidate for zoning using one system. The key here is finding a competent dealer who has demonstrated experience in zoning both in equipment, proper sizing, and ductwork design. If going this route, I would want a total integrated system and controls like Carrier Infinity or Bryant Evolution. I suggest getting references and visiting similar installs to discuss with homeowners.

IMO

Yes Natural Gas Furnace for Heating along with the AC condenser.

I have read up a lot on zoning, it seems to me like there are not a lot of installers in the industry that really know how to set them up properly. There also is a lot of negative information on zoning as it relates to the troubles a by-pass can cause to your systems efficiency.

That is why I was leaning towards the two unit system, however need to figure out the proper size for each level. I know the best thing to run is a Manual J on the place however as a starting point what is the general rule based on square footage in determining the tonnage and BTU for a heating and cooling system? That along with how does the rising of hot air and the dropping of cool air determine the size you would go with? Any help would be appreciated.

I agree for a house of your size two HVAC systems is the best way to get consistent temperatures on both floors. I also believe two smaller systems operate more efficiently and have a longer life than one large zoned system. If it were my house I would install both furnaces in the basement and add a chase to bring the duct work up to the second floor.

For a new build you must do a Manual J calculation. The rules of thumb don't work with the insulation values you are using. The calculation takes into account if the floor above or below is conditioned space or not. The software to do your own calculation is available on line for $50.

Do you have link to the software?

~Gary

Here is the link. I have never used it but posters have reported good results.

Here is a link that might be useful: HVAC Calc