The kinetic energy of macroscopic motions in the atmosphere is most probably not simply related to total kinetic energy of molecular motions (which is many times higher), but is rather linked to the intensity and location of air heating due to radiation and air humidification due to oceans. For example, the air in my room (windows and door closed) has, in a simple model, around 10 MJ of kinetic energy of molecular motion. Since the convection is weak, the kinetic energy of macroscopic motion is many times lower, probably less than 1 J. When I open the window and let the dense cold air in, the hot air gets out and much stronger convection sets in. The macroscopic kinetic energy is now much higher than before, both due to higher density and higher speeds of flow, but still nowhere near those 10 MJ. As a result, I have more energy in the room, but lower temperature. Of course, the weather is much more complicated, but you get the idea.