In this paper we propose a multiscale traffic model, based on the family of Generic Second Order Models, which integrates multiple trajectory data into the velocity function. This combination of a second order macroscopic model with microscopic information allows us to reproduce significant variations in speed and acceleration that strongly influence traffic emissions. We obtain accurate approximations even with a few trajectory data. The proposed approach is therefore a computationally efficient and highly accurate tool for calculating macroscopic traffic quantities and estimating emissions.