In this paper, we focus on the implementation and verification of an extended Boussinesq model for surf zone hydrodynamics in two horizontal dimensions. The time-domain numerical model is based on the fully nonlinear Boussinesq equations. As described in Part I of this two-part paper, the energy dissipation due to wave breaking is modeled by introducing an eddy viscosity term into the momentum equations, with the viscosity strongly localized on the front face of the breaking waves. Wave runup on the beach is simulated using a permeable-seabed technique. We apply the model to simulate two laboratory experiments in large wave basins. They are wave transformation and breaking over a submerged circular shoal and solitary wave runup on a conical island. Satisfactory agreement is found between the numerical results and the laboratory measurements.