If you've put your intermediate files in a location other than your WPS directory, you can use the namelist.wps parameter "fg_name" to show not only the prefix name, but also a path to those files. For e.g., if your files had the prefix "CMIP6" and you had them in a directory /home/user/int_files, you could setI am also facing the same issue. I created CMIP6 intermediate files, but how to set those files path in namelist.wps for running metgrid.exe [I can copy those files into em_real directory, but there are a large number of files, so if I can handle it in a separate directory it will easy.
fg_name = '/home/user/int_files/CMIP6'