Visualizations in interactive computer simulations are a powerful tool to help students develop productive mental models, particularly in the case of quantum phenomena that have no classical analogue. The QuVis Quantum Mechanics Visualization Project develops research-based interactive simulations for the learning and teaching of quantum mechanics. We describe efforts to refine the visual representation of a single-photon superposition state in the QuVis simulations. We developed various depictions of a photon incident on a beam splitter, and investigated their influence on student thinking through individual interviews. Outcomes from this study led to the incorporation of a revised visualization in all QuVis single-photon simulations. In-class trials in 2013 and 2014 using the Interferometer Experiments simulation in an introductory quantum physics course were used for a comparative study of the initial and revised visualizations. The class that used the revised visualization showed a lower frequency of incorrect ideas about quantum superposition, such as the photon splitting into two half-energy components.