The perception of an ambiguous stimulus rely on the activation of multiple cortical areas, operating a sensorimotor transformation along the cortical hierarchy. Furthermore, choice related information is found as upstream as the primary sensory areas, suggesting bi-directional communication at all stages of the cortical hierarchy. How do sensory and choice related activities flow and organize across multiple brain areas? Here, we designed a two-alternative forced-choice task (2AFC) in which mice compared stimulation frequencies applied to two adjacent vibrissae. Using two-photon functional imaging, we simultaneously studied the activity of layer 2/3 neurons in the primary (S1) and secondary (S2) somatosensory areas. We found that the representations of stimuli versus choice are independently encoded in each of the two cortical areas. Between areas, a dynamic causal modeling (DCM) analysis revealed weighted, bidirectional (S1-S2) flow of sensory activity and a top-down only (S2 to S1) flow of choice related activity. Sensory versus choice flows of activity appeared independent and non-interacting, thus seemingly relying on communication channels lying in different dimensions. In addition, we found modulations of sensory information processing when the animal is performing the task versus a passive condition, including: (1) an improvement in sensory encoding within S1 and (2) an increase in redundancy of sensory information between areas S1 and S2. In conclusion, this study highlights the complex interplay between sensory and high-level cognitive processes across cortical areas, revealing distinct encoding patterns, feed-forward and top-down information flows, and adaptive modulation of sensory processing during task performance.