A system and method for operating an engine having at least two spark plugs per cylinder include controlling at least one actuator to alter combustion within a selected cylinder such that the combustion burn rate determined by ion sense current signals associated with the at least two spark plugs of the selected cylinder approaches a desired combustion burn rate. A desired combustion burn rate is determined based on current engine/vehicle operating and ambient conditions with ion sense signals from each spark plug analyzed to determine combustion timing relative to corresponding ignition timing. Ignition timing and/or other actuators are controlled in response to provide a desired combustion burn rate.