The dynamics of the upper atmosphere is strongly affected by the coupling between the magnetosphere, ionosphere and thermosphere, especially during the magnetic storms and magnetospheric substorms. It is now well recognized that the additional energy input from the magnetosphere during such magnetically active times can not be neglected while determining the heat and energy balance of the upper atmosphere which creates pronounced effects on the atmospheric circulation at high altitudes. One of the long standing problems of the MIT coupling is the determination of the neutral wind and its effects on the Joule Heating of the upper atmosphere. In this study, we derive spatial distributions of the neutral temperatures and neutral wind drift velocities at different heights from GITM and TIEGCM runs. A quiet day, without magnetic activity is also studied with TIEGCM to give the background variations in the environment where the substorm related neutral winds are superimposed upon. Initial results from the models demonstrate clear differences in the magnitude, altitude and latitudinal variations of the upper atmospheric temperatures and the neutral wind velocities which consequently have effects on the Joule Heating.