In this paper, we focus on the modification of policies that can lead to movement patterns and directional guidance of occupants, which are represented as agents in a 3D simulation engine. We demonstrate an optimization method that improves a spatial distancing metric by modifying the navigation graph by introducing a measure of spatial distancing of agents as a function of agent density (i.e., occupancy). Our optimization framework utilizes such metrics as the target function, using a hybrid approach of combining genetic algorithm and simulated annealing. We show that within our framework, the simulation-optimization process can help to improve spatial distancing between agents by optimizing the navigation policies for a given indoor environment.