There is a science to the duct work in a furnace distribution system. For instance, if you vent a duct off the end of a plenum you will get more heat than taking the same vent off the side of the same plenum line. This is usually not something you have control over so here are some approaches you can use instead. First of all try to measure the air flow from the vents. If some vents are hotter and have more force it may be enough to partially close the grill in the floor or ceiling to hold back the heat. If the vent is weak you can buy inline fans to boost the air flow. If the air is cool you may be able to insulate the line somehow to keep the heat in.