You need to make sure that they provided some type of safety interlock between the two units or that they installed a backflow damper in the 2 ton duct. When the furnace operates with out the 2 ton air handler running the hot air will flow backwards through the 2 ton AH and be returned to the furnace. This will cause the furnace to become very inefective and HOT.
Are you confident that the zoning system is functioning properly? Dampers open and close when appropriate, equipment operates when thermostats are calling?
"When you perceive zoning not as a bandage but as an enhancement, you truly understand the dynamics and limitations of forced air heating and cooling"