EnergyPlus performs separate heat balances for the outside surface (short-wave solar + long-wave thermal + convection + conduction) and the inside surface (long-wave radiation from surfaces + short-wave radiation from lights + long-wave radiation from equipment + conduction + transmitted solar from outside surface + convection). The links will take you to the Engineering Reference for more info on the equations.

You can customize the surface thermal resistance with multiple surface property objects in EnergyPlus. Some examples of these objects are:

• SurfaceConvectionAlgorithm:Outside and SurfaceConvectionAlgorithm:Inside: Lets you choose how convection coefficients are calculated
• SurfaceProperty:ConvectionCoefficients and SurfaceProperty:ConvectionCoefficients:MultipleSurface: Lets you input specific values EnergyPlus will use for convection coefficients (EnergyPlus will not calculate them)
• SurfaceProperty:OtherSideCoefficients: Lets you set a list of possible surface attributes, including combined convective / radiative film coefficient or constant surface temperature. Note that solar effects are not accounted for on the referenced surface.

EnergyPlus calculates U-value using the thermal resistance values of each material layer within the surface's construction assembly, the inside surface film resistance, and the outside surface film resistance. To see the end results of the EnergyPlus U-value calculations, you should include the Envelope Summary Table in your list of outputs.

You should also check out the Engineering Reference document for how EnergyPlus handles window heat balance calculations differently than opaque surface heat balance calculations.