In this paper we test and apply the master equation approaches developed in paper I. We demonstrate that our master equation methods can greatly improve upon the performance of more standard approaches, rendering nearly quantitative agreement compared to numerically exact tests under a variety of conditions. The methods developed in paper I are also demonstrated to be fully capable of handling the effects of nonequilibrium initial preparation, which can be quite prominent at short times. This property is used to study the kinetics of photoinduced charge transfer in a mixed valence compound. For this system, we discuss observed short-time nonexponential behavior, dynamical trapping, and coherence. Last, we discuss the significant computational advantages of our methods in terms of their scaling with the number of discrete states in the system.