In one aspect, an engine controller for an engine including multiple working chambers is described. The engine controller includes a mass air charge determining unit that estimates a mass air charge or amount of air to be delivered to a working chamber. Firing decisions made for a firing window of one or more firing opportunities are used to help determine the mass air charge. The engine controller also includes a firing controller, which is arranged to direct firings to deliver a desired output. Fuel is delivered to a working chamber based on the estimated mass air charge.