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Yes - you can do that. You can either include process emissions under the Non Energy tree branches or you can enter them (if relevant within the energy sector branches). The former approach is more in-line with the IPCC's accounting methods, but the latter approach can sometimes be useful if the process emissions are directly connected to the same activities being modeled in the energy sector or to the scale of energy use therein. For example, process emissions from cement are directly related to cement's overall levels of production and energy use. Fugitive emissions from oil and gas are similar.
When setting up process emissions under the demand branches you may want to specify the method as "total annual loading" rather than as per unit of energy consumed. That way you have more flexibility and can also make use of additional user defined variables to do further modeling. See screenshot.
I'm afraid there are no default emission factors for process emissions yet. Various efforts under way to improve the default data in LEAP though. Stay tuned!