A variety of methods and arrangements are described for controlling transitions between firing fractions during skip fire or other dynamic firing level modulation operation of an engine. In general, actuator first transition strategies are described in which an actuator position (e.g., cam phase, TCC slip, etc.) is changed to, or close to a target position before a corresponding firing fraction change is implemented. When the actuator change associated with a desired firing fraction change is relatively large, the firing fraction change is divided into a series of two or more firing fraction change steps. A number of intermediate target selection schemes are described as well.