Ernesto,
Smkinven has a flag called "NETCDF_POL_UNIT” to specify the unit of the EDGAR pollutants, set to kg m-2 s-1 which is consistent to your setting.
Also, you have an option how to process your inventory as monthly or annual based on your knowledge. You can tell Smkinven how to handle them by how you setup the Smkinven inventory list input file (ARINV). Here is the format shown below. You need to put either specific month (i.e., 1, 2, 3,12) if your inventory file is monthly. If it is annual, then set it to 0.
#SCC, Pollutant, Variable_Name, Month, File_location_name
SOLVENT,VOC,emis_nmvoc,0,/nas/EDGAR/solvent/nmvoc/v42_2010.nc
SOLVENT,CH4,emis_ch4,0,/nas/EDGAR/solvent/ch4/v42_2010.nc
ENERGY,NOX ,emis_nox,0,/nas/EDGAR/energy/nox/v42_2010.nc
ENERGY,PM25,emis_pm25,0,/nas/EDGAR/energy/pm2.5/v42_2010.nc
ENERGY,NOX,emis_nmvoc,0,/nas/EDGAR/energy/nmvoc/v42_2010.nc