Please respond with the square footage of your house on each floor, efficiency rating, btu rating, and tonnage rating of heater/ac, the brands (which makes a big difference), how much the quotes are for. Also are they replacing any ductwork?
Also consider insulating the walls. A high efficiency furnace doesn't seem to jive with low efficiency walls. If available funds is a factor, I would take the money saved by buying less efficiency and put it into wall insulation (blown, etc).