There are many methods to calculate the heat gains from a glazing element. Typically the heat gains are divided into two components, the Conduction related to the Uvalue and the Radiation related to the SHGC. Dividing the heat gains in this fashion is helpful because it allows key characteristics of the glazing, Uvalue and SHGC, to be considered in regard to their impact on cooling loads.
Focusing on Conduction
Conduction gain or loss can be calculated in various methods with different degrees of detail. The simplest calculation method is to consider the uvalue, area, indoor, and outdoor temperature as described by Equation 14, ASHRAE Handbook Fundamentals Chapter 18.
Q = U * A * (Tout  Tin)
This method accounts for the thermal transmittance of the element and the respective temperatures and is very helpful for hand calculations.
EnergyPlus uses the Heat Balance method for calculations, which covers four specific heat transfer processes in a building:
Outdoor face heat balance
Wall conduction process
Indoor face heat balance
Air heat balance
The Heat Balance method is defined in ASHRAE Handbook Fundamentals Chapter 18 and is a well established and widely used method for cooling load calculations. In EnergyPlus, the Heat Balance methodology is applied to windows or glazing elements. Currently windows in the calculation default to a single layer which represents the performance values. A brief summary of the input variables and equations is included at the end of this article. In addition, here are links to the full documentation of the Windows Module and Window Heat Balance Calculation.
Glazing Result Variables
EnergyPlus produces several output variables for every element of the model. This allows for powerful study of heat, energy, and radiation transfers throughout the building. Full documentation of the window outputs from EnergyPlus can be found here. For a window without interior shading the total heat flow is equal to:
Surface Window Transmitted Solar Radiation Rate
Convective heat flow to the zone from the zone side of the glazing
Net IR heat flow to the zone from zone side of the glazing
Shortwave radiation from zone transmitted back out the window
Convection to zone from window frame and divider, if present
A good way to think about this is the sum of the solar and conductive gain to the zone from the window.
Glazing conduction results are reported for Rooms, Zones, and Air Systems on the platform. Checkout more about the load modeling results here.
Glazing Heat Balance Equations
Summary of variables, equations, and diagram explaining location of the variables. Full description of the method can be found here.
Mathematical variable  Description  Units 
N  Number of glass layers   
α  StefanBoltzmann constant 

εi  Emissivity of face i   
ki  Conductance of glass layer i  W/m2K 
ho, hi  Outside, inside air film convective conductance  W/m2K 
hi  Conductance of gap j  W/m2K 
To, Ti  Outdoor and indoor air temperatures  K 
Eo, Ei  Exterior, interior longwave radiation incident on window  W/m2 
θi  Temperature of face i  K 
Si  Radiation (shortwave, and longwave from zone internal sources) absorbed by face i  W/m2 
Iextbm  Exterior beam normal solar irradiance  W/m2 
Iextdif  Exterior diffuse solar irradiance on glazing  W/m2 
Iintsw  Interior shortwave radiation (from lights and from reflected diffuse solar) incident on glazing from inside  W/m2 
Iintlw  Longwave radiation from lights and equipment incident on glazing from inside  W/m2 
φ  Angle of incidence  radians 
Afj  Front beam solar absorptance of glass layer j   
Af,diffj, Ab,diffj  Front and back diffuse solar absorptance of glass layer j   
A, B  Matrices used to solve glazing heat balance equations  W/m2, W/m2K 
hr,i  Radiative conductance for face i  W/m2K 
Δθi  Difference in temperature of face i between successive iterations  K 
Glazing system with two glass layers showing variables used in heat balance equations. Source: EnergyPlus 22.2 Engineering Reference manual
The four equation used in the heat balance calculation are: