An integrated inertial motion capture system includes external position aiding such as optical tracking. The integrated system addresses and corrects misalignment between the inertial (relative) and positioning reference (external) frames. This is especially beneficial when it is not feasible to rely on magnetometers to reference the heading of the inertial system. This alignment allows effective tracking of yaw in a common reference frame for all inertial sensing units, even those with no associated positional measurements. The disclosed systems and methods also enable an association to be formed between the inertial sensing units and positional measurements.