If you have your own analysis data that includes rain, snow, cloud water, etc., you can include these variables in the met_em* files. If you have gribbed data, you will simply run it through the ungrib.exe program, and then run metgrid.exe using that data, plus whatever other data you used for initial and boundary conditions. This will alert to metgrid.exe program using various flags (e.g., FLAG_QC, FLAG_QR, etc.) that will automatically tell the real.exe program to process these variables, and save them in the wrfinput* files. Once wrf.exe begins to run, these variables will be read and taken as their intial value.