An integrated sensor system for use in a furnace system including a furnace having at least one burner and two or more zones each differently affected by at least one furnace parameter regulating energy input into the furnace, including a first temperature sensor positioned to measure a first temperature in the furnace system, a second temperature sensor positioned to measure a second temperature in the furnace system; and a controller programmed to receive the first and second measured temperatures, and to adjust operation of a furnace system parameter based on a relationship between the first and second temperatures, thereby differentially regulating energy input into at least two of the zones of the furnace; wherein the relationship between the first and second temperatures is a function of one or more of a difference between the two temperatures, a ratio of the two temperatures, and a weighted average of the two temperatures.