I agree with others. Its probably a simple fix and if at all handy, you can fix it yourself and save the headache of taking it back to the dealer.
First off, if 2 air conditioners and 2 thermostats its highly unlikely that the one in the upper level has anything to do with the gas furnace. If it has a heat choice on it, its most likely to control the heat pump option (if equipped) on the front a/c unit. If you do not have a heat pump option, then the heat setting on that thermostat is inop.
The thermostat in the main room should control only the main level roof unit and furnace.
Finally, the heat flow to the upper level on fivers is generally always pretty poor but you should get some flow.
Like other have said, its likely a crushed or loose duct OR the duct is disconnected at the furnace.
I think it will be a simple fix.
