A good solution is separate headers for each zone, with flow controllers (actuated vanes) in the inlet of each header. You can have as many headers (zones) as you want to subdivide. The only additional cost is the ducting and the temperature/controller/vanes per header.
Each zone would have a thermostat controlling the vanes in each of the header. In summer, when cooling, the warmer zones would get more flow. In winter, the cooler zones would get more flow.
Aside from upstairs vs downstairs zoning, don't forget the effect of sun exposure. The souther exposure is warmer than the northern. The side with more windows is usuall warmer during daylight than the side without the windows. You may decide that there are actually 4 zones in your 2 story. Up north, up south, down north, down south.
"Do not worry about your problems with mathematics, I assure you mine are far greater."
Albert Einstein
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