Letting the furnace control low/high fire rather than the thermostat is usually preferable. Forcing the furnace to run on low fire when your heat loss is too great (colder weather) will result in a drafty feeling due to the warm air temp being too low. On many systems I installed the main thermostat recorded the time that the furnace ran in low and high fire as well as low and high cooling among other statistics. I found that the system ran in low fire about 70% of the time. It's also worth mentioning that the variable-speed blower will adjust it's speed to match the heating mode (and provide the proper air temp) saving a significant amount of $ for electricity. Please do NOT use the G (green wire) terminal to test the use of W2 (2nd stage heat) as mentioned above...it can cause numerous problems.