Depending on where you are located, the federal, state and local regulations, what volumes you are processing, what processes you are using and what chemicals are used in those processes, you may be required to do nothing, register as an emission source, or get a permit (there are 2 or more permits available depending on total emissions).
If you are required to get a permit (usually total emissions have to total 10 tons per year or more) you will also need to at least submit an annual emissions report. That is where the AP-42 emissions calculations come in (for natural gas combustion), plus your emissions estimates for process pollutants (based on reasonable estimates such as mass based calculations).
IF you are considered a major source, 100 tons per year or greater, there are much greater hurdles to get through. Not many precious metal refiners fall into this category.
If you fall into the permit category, you will need the help of an environmental engineer because you will be doing pollutant modeling to submit with the permit application.