This is my first post here, but you all have helped me a lot in the past.

My question has to do with the multiple HVAC systems in our house and if they are functioning together correctly. A little background information. We bought the house about 2 years ago with everything already installed. There is a HRS with HEPA filtration, 2 zones with honeywell controls, and Bryant gas furnace (i95 model I think) with variable speed fan, and Braynt AC. My problem is in our ranch home with walkout basement and open stairway, the temperature difference between the upstairs and downstairs can be upwards of 10 degrees when the AC is on, even when the downstairs zone is completely off. Our infant's and toddler's rooms are both downstairs and we constantly battle between freezing them out and making it comfortable for my wife and I to sleep upstairs. We keep their vents closed and their doors shut, but enought air gets past the zone control to keep it really cold. I thought that running the thermostats in fan on mode would help distribute some of the cool air downstairs to the upstairs. When I did this, though, I realized that when in fan on mode, only the fan on the HRS was running, not the air handler, and therefore moving very little air around the house. Of course when either heat or AC is called for, the air handler kicks on. Does this sound right? I would have thought that in fan on mode, the air handler would run non stop, without the HRS as we are not really looking to introduce fresh air at that time. Can anyone confirm that my train of thought is correct?