Gabe,
You can modify either geo_em.nc or wrfinput_d01. Note that land use change may also be related to other variables like vegetation fraction, leaf area index, etc. If you set rdlai = .false., then LAI will be derived from the VEGPARM.TBL based on the land use type. This will make things less complicated. However, vegfra (in wrfinput) or greenfrac (in geo_em) needs to be changed if land use is changed.
NCL or the utility we provide can be used to modify the variables.
For NCL, you can find the example here: https://www.ncl.ucar.edu/Applications/change_netCDF.shtml
For WRF utility, please go to: http://www2.mmm.ucar.edu/wrf/users/utilities/util.htm, where you can click read_wrf_nc and find how to use it to change variables in netCDF file.