Hi Ahmad -
I suggest adding a methane emission factor to the natural gas fuel consumed in your Transmission and Distribution module, and in the Avg Environment Loading variable for methane, select the "Per Unit Energy Lost" method (this is adjacent to the units selection box). You're correct that the denominator of the emission factor must always be in energy units (ex. kilograms per terajoule lost), so you would enter a value which is exactly the energy density natural gas, measured in kg/TJ or whichever appropriate units.
Hope this helps,
Taylor