Will I see any performance gains if I reconfigure my thermostat to control the second stage of my 2 stage furnace?
Without the thermostat telling it, the furnace has to guess how much heat you need, and those guesses may not always be right. The thermostat will know how far you from your target temperature and know which stage you need to be using. That means a thermostat wired up for both stages will heat up faster when you get back from vacation, and the temperature stays more constant all other times.