We present a new approach for simulating the atmospheric dynamics of the close-in giant planet HD209458b that allows for the decoupling of radiative and thermal energies, direct stellar heating of the interior, and the solution of the full three-dimensional Navier-Stokes equations. Simulations reveal two distinct temperature inversions (increasing temperature with decreasing pressure) at the sub-stellar point due to the combined effects of opacity and dynamical flow structure and exhibit instabilities leading to changing velocities and temperatures on the nightside for a range of viscosities. Imposed on the quasi-static background, temperature variations of up to 15% are seen near the terminators and the location of the coldest spot is seen to vary by more than 20°, occasionally appearing west of the anti-solar point. Our new approach introduces four major improvements to our previous methods including simultaneously solving both the thermal energy and radiative equations in both the optical and infrared, incorporating updated opacities, including a more accurate treatment of stellar energy deposition that incorporates the opacity relevant for higher energy stellar photons, and the addition of explicit turbulent viscosity.