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I assume that you are referring to the Site and Source Energy table of the Annual Building Utility Performance Summary (ABUPS) table report. An example screen shot of this table is below.

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Example Site and Source Energy Table

Site energy is what is consumed by the building site. Source energy is what is consumed by utilities and other entities in order to supply that energy consumed by the building site. The ratio between these is called the site-to-source conversion factor, which is different for each resource consumed and shown in the Site to Source Energy Conversion Factors table in the same ABUPS summary report (see below).

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Example Site to Source Energy Conversion Factors Table

These conversion factors can be set using FuelFactors and EnvironmentalImpactFactors objects.

To answer your second question, Total Site Energy is the "gross" energy consumed by the building site and Net Site Energy is the final energy consumed by the building site after accounting for any on-site energy generation (photovoltaics, generators, etc.). In my example table above, there is no on-site energy generation, so total and site energy use are the same.