Hi,
You should be able to copy the em_convrad directory, and name is something different (e.g., em_convrad_2), and the copies directory will contain the same files and executables link back to the WRF/main/ directory. However, if you want to run them simultaneously, you may want to copy the executables (ideal.exe and wrf.exe) from the main/ directory, to the individual directories, instead of keeping them linked. It may not make any difference, but I'm not sure what happens if you try to use the same executable at the same time.