In an air handling system of a uniflow-scavenged, two-stroke cycle opposed- piston engine, one or more engine operating state parameters are sensed, numerical values of air handling parameters based on trapped conditions in a cylinder of the engine at the last port closing of an engine operating cycle are determined in response to the sensed parameters, the numerical values are evaluated, and one or more of the numerical values is adjusted in response to the evaluation. The adjusted numerical values are used to control charge air flow and EGR flow in the air handling system.