I do not think you will need any USGS software for this. You will need to use the WRF Pre-processing System (WPS) to build your WRF-Hydro domain file (
geo_em.do1.nc) and to pre-process inputs such as landcover. WPS (specifically geogrid.exe) will build your domain and interpolate fields from a collection of tiled geospatial datasets. There are two supported landcover classifications systems, USGS and MODIS, so you will need to select the geospatial dataset that represents your desired landcover classification system. You can look at the index files for each tiled dataset to find information such as the classification system. Below I have provided some links that you may find useful as you create your WRF-Hydro domain.