Internal combustion engine having cam actuated valves that can be controlled to facilitate the use of different air charge levels in different cylinders or sets of cylinders are described. In one aspect a first set of cylinders is operated in a skip fire manner in which the corresponding cylinders are deactivated during skipped working cycles. Cam actuated intake valves associated with a second set of cylinders are operated differently so that the air charge in the cylinders in the second set is different than the air charge in fired cylinders subject to the skip fire control. According to another aspect, an engine having cam actuated intake valves is operated in a dynamic firing level modulation mode. During the dynamic firing level modulation operation, the cam actuated intake valves are controlled in at least two different manners to such that different cylinder working cycles have different air charges.