We have a new two storey home 2700 sqft with a open 15x15 ft open area common to both the main floor and top floor. We have two furnaces one is dedicated to the top and one to the main floor with infloor htg in the basement. If the bottom floor furnace runs it minimizes the top floor furnaces running time and amount of cycles and vice versa with the main floor furnace. Our master bed rm is over the garage which has six registers we keep the doors closed due to pets. When the top flr furnace runs it cooks us out because the thermostat is on a wall in the hall. We have two fans on the top floor and have tried both fan directions at low speeds one is in the loft area and one in our bonus room adjacent to loft. Running these fans doesn't seem to help. We have a heat register close to the upper floor thermostat and directly across from it is a cold air return which when the cold air return is left open the furnace runs 2-3 minutes when plugged the furnace will run 7- 10 minutes. We have programmable thermostats and run the mainfloor at 22- 23 degrees c and the top floor at 20-21 degrees c if any more it will be above 25 in our bedroom. On the top floor we have two kids bedrooms and one bathroom the loft and the master bedroom equaling 1375 sgft. We have one register and cold air return in each kids bedroom and one under cabinet register in the bathroom one in the loft and one in the bonus room and six in the master bed room. We just cannot get this house comfortable. We questioned why we only have one register in the bonus room (15 x 15 area with three 3x3 windows) also the great room(20 x 20) below the loft has windows for walls on the south and west sides reaching from the main floor to the ceiling these windows are the solar e type. We are debating whether the thermostats should be relocated or pushing the builder to add another register to the bonus room or we might have a negative pressure problem. (candles flicker even when no fans or furnaces running) when we come in from the garage our french doors in the master bedroom upstairs pop open. Is there any slutions to our problem maybe its an operational issue.