New wearable devices and technologies provide unprecedented scope to augment or substitute human perceptual abilities. However, the flexibility to reorganize brain processing to use novel sensory signals during early sensitive periods in infancy is much less evident at later ages, making integration of new signals into adults’ perception a significant challenge. We believe that an approach informed by cognitive neuroscience is crucial for maximizing the true potential of new sensory technologies. Here, we present a framework for measuring and evaluating the extent to which new signals are integrated within existing structures of perception and experience. As our testbed, we use laboratory tasks in which healthy volunteers learn new, augmented perceptual-motor skills. We describe a suite of measures of (i) perceptual function (psychophysics), (ii) neural representations (fMRI/decoding), and (iii) subjective experience (qualitative interview/micro-phenomenology) targeted at testing hypotheses about how newly learned signals become integrated within perception and experience. As proof of concept, we provide example data showing how this approach allows us to measure changes in perception, neural processing, and subjective experience. We argue that this framework, in concert with targeted approaches to optimizing training and learning, provides the tools needed to develop and optimize new approaches to human sensory augmentation and substitution.