Using a dynamic density functional theory, we study the charging dynamics, the final equilibrium structure, and the energy storage in an electrical double layer capacitor with nanoscale cathode-anode separation in a slit geometry. We derive a simple expression for the surface charge density that naturally separates the effects of the charge polarization due to the ions from those due to the polarization of the dielectric medium and allows a more intuitive understanding of how the ion distribution within the cell affects the surface charge density. We find that charge neutrality in the half-cell does not hold during the dynamic charging process for any cathode-anode separation, and also does not hold at the final equilibrium state for small separations. Therefore, the charge accumulation in the half-cell in general does the surface charge density and the charge accumulation within the concentration, cathode-anode separation, and applied voltage. For which the charge accumulation exceeds the surface charge at special density has a maximum at intermediate electrolyte concentrations not equal the surface charge density. The relationships between half-cell are systematically investigated by tuning the electrolyte high electrolyte concentrations, we observe charge inversion at special values of the separation. In addition, we find that the energy for a high applied voltage.