An understanding of how students develop and use representational competence skills requires a holistic account of the nature and interactions of multiple complex factors. Schönborn and Anderson proposed an empirical model that suggests that learning with representations is affected by the nature of the given representation (mode), scientific knowledge of relevance to that representation (conceptual), cognitive skills that a student must utilize to make sense of that representation (reasoning), as well as the interactions between these factors. As suggested, student overall ability to develop representational competence skills depends on both the engagement of all three factors (i.e., conceptual-reasoning-mode) and the nature of the contribution of each factor when students employ various representational competence skills (e.g., whether scientifically sound or unsound conceptual knowledge and reasoning is used). In this project, we employ Schönborn and Anderson’s model to characterize how organic chemistry students make sense of various representations of chemical structure (e.g., dash-wedge diagrams, Newman projections, and chair conformations). Given that this model has been previously expressed in the context of biochemistry (e.g., representations of antibody-antigen interactions), this study tests this model in the novel context of organic chemistry representations. Additionally, the model has been positioned as explaining students’ ability to interpret representations. We explore new applications of this model to explain how students engage in other representational competence skills, such as the ability to translate between representations and the ability to use representations to make inferences about chemical phenomena.