This paper uses a generative neural network architecture combining unsupervised (generative) and supervised (discriminative) models with a model comparison strategy to evaluate assumptions about the mappings between brain states and behavior. Most modeling in cognitive neuroscience publications assume a one-to-one brain-behavior relationship that is linear, but never test these assumptions or the consequences of violating them. We systematically varied these assumptions using simulations of four ground-truth brain-behavior mappings that involve progressively more complex relationships, ranging from one-to-one linear mappings to many-to-one nonlinear mappings. We then applied our Variational AutoEncoder-Classifier framework to the simulations to show how it accurately captured diverse brain-behavior mappings,provided evidence regarding which assumptions are supported by the data, and illustrated the problems that arise when assumptions are violated. This integrated approach offers a reliable foundation for cognitive neuroscience to effectively model complex neural and behavioral processes, allowing more justified conclusions about the nature of brain-behavior mappings.