We are developing plans for a 2500 sq ft bungalow with two distinct zones of 1000 and 1500 sq ft. We would like to control heat and a/c in each zone. We will be using a high efficiency oil furnace for heat installed in the basement. Dual zone systems are not yet common in our area (Eastern Ontario). Any suggestions on system configuration, especially appropriate controls, would be greatly appreciated.

Advice is as follows
Do a manual J On your future home. You van use your plans

Do a manual D On your home You can use your plans

Then and only then start to consider various control types.

The reason for this is at last count there are 22 companies that make different types of controls for zoning. You will need the above information in order to pick the best control for your situation.
I could write a book time does not allow that.
I will make this statement. If you have to have by pass dampers for duct and you will if you continue to want to use one furnace Take a look at Fan handler for your blower speed reduction. It is automatic and will slow the blower up when any damper closes to prevent excess blower noise and the problems with too much air flow on the ac side.

My solution is as follows. Use a boiler and separate hot water air handlers for your different Zones. This way you will have complete control of your two systems separately. You will also be using to different outside A/C units but the nice part about this system is.

You can use heat pumps instead of strait cooling units.
This will chop you overall fuel cost by about 30% or more.

Having two systems means that if a problem comes up in one part of the house you will still have heat and A/C in the other. That is of course if the boiler does not break down in the heat season.

95% boilers are available for oil. Check Peerless Boiler Company.

Look into two separate systems with two furnaces. Use a heat pump for primary and the oil furnace as the secondary. This may cost a little more to install but will save in operating costs and give you two completely separate zones. Good luck to you, Mike

I forgot to ad that you can get your hot water for shower,dishwasher or any other water needs from your boiler and you will have a super recovery rate. Two oil furnaces like actec said will work also but they will require two class (A) chimneys etc and you get no hot water out of the deal.