For central A/C, you'll need ducts and vents. Once you have the ducting in place anyway, you might as well use it for both your heating and cooling.
For a three floor house, you definitely want some kind of zoned system, with a thermostat on each floor. (I wish my 2-floor house was zoned.) You may want multiple cooling systems, or maybe one system with motorized dampers to control airflow to the various floors. Your HVAC contractor should be able to make a reccomendation of what will work best.
Whatever you do, do not skimp on the ductwork. Your HVAC contractor should run calculations on how big the ducts need to be. For many home builders, HVAC is a minor concern in the bulding plan. Make sure everything is sized correctly. Changing ductwork after the fact is very difficult. And if you don't have proper ducting, it won't matter how good your central heating using is.
For new construction, Geothermal is usually a good candidate. It can provide heating, cooling, and hot water with crazy efficiency. The installation cost is MUCH higher though. (There are tax credits that will offset some of the cost.) If you aren't up for geothermal, I would go for a traditional air-sourced heat pump for your heating and cooling needs. They are pretty efficient (at least in moderate climates). You are pretty much in the perfect lattitude for a heat pump.
However, I would not have the heat pump (air-sourced or geothermal) as your only heating system. Some kind of alternate (non-ducted) heat source would be a good idea. Heated floors, gas fireplace, etc. Air-sourced heat pumps lose their efficiency in very cold weather. And it can also be nice to have gentle air convection, vs a duct that is blowing in your face. You also have a backup system in case your central heat fails.
That said, ducted air is nice, because some regular circulation of air in all the rooms of the house avoids that "stagnant air" smell, as well as cutting down on dust, dander, etc.
Also, central air systems give you options for humidification and de-humification of the whole house. Look into that. It is usually a minor cost increase in the system, but can make a major difference in comfort.
In the UK, the term I'd associate is "bleeding the radiators", and there will be a little valve at the top of each radiator to release trapped air, something a little like:
These are typically operated with a "bleed key" (the brass object resting on the fins of that radiator), or sometimes the valves are also slotted for use with a screwdriver - they typically require less than a quarter turn to operate, and you'll either hear the air hissing out, or see water dribbling through - Always have a cloth or rag held close and tight to the radiator as water will come out once the air has gone.
With regards to picking an order, every system is different, and you'll come to learn which radiator tends to fill with air first (so in my case, it's the one on my upstairs landing, next to the hot water cylinder cupboard, but in my parents house, it's the one in their downstairs hallway). As the system is new to you, it may just be a case of doing each in turn.
You should check the pressure after bleeding, especially if there was a significant amount of air trapped.
Best Answer
The "Registers" on the blowy holes are adjustable down to fully closed. The Grills on the sucky holes are not adjustable. You should find that the middle room's Register can be almost completely closed in order to maintain an even temperature equal to the other rooms.
Unfortunately, this adjustment or setting only applies to heating as you discovered upon switching from cooling. You'd need to either manually set the middle room's Register each heating &/or heating season or have a programmable & motorized External Register or Internal Damper installed to do it for you.