Add the following to user_nl_cam:
&chem_inparm ext_frc_specifier = '$species_name1 -> $path_to_vertically_gridded_emissions, $species_name2 -> $path_to_vertically_gridded_emissions' srf_emis_specifier = '$species_name1 -> $path_to_surface_emissions, $species_name2 -> $path_to_to_surface_emissions' srf_emis_type = 'SERIAL' /
Make sure to add all the emissions you need. The example of default emissions can be found in CaseDocs/atm_in after a default build. Re-building the model will update the emissions to the new definitions. If you want to repeat emissions from one year over variable dynamics use:
&chem_inparm srf_emis_type = 'CYCLICAL' srf_emis_cycle_yr = $YYYY / &chem_surfvals_nl flbc_type = 'CYCLICAL' flbc_cycle_yr = $YYYY /
Another example is in the CAM6 user guide.