Thanks to Rick Brownrigg from UCAR, there is a way to draw features from shapefiles (arcGIS) into NCL codes, an example in (#3 in particular):http://www.ncl.ucar.edu/Applications/shapefiles.shtml
this NCL code uses the 'gsn_add_polyline' function. then I overlapped the boundary layers (from a shapefile) to my WRF results. keep in mind that every time you use a 'wrf_map_overlays' function that by default advances the frame. so it's necessary to modify NCL with (thanks to Mary Haley):
pltres@FramePlot = False
pltres@PanelPlot = False
then both layers will be in the same frame and you see your WRF results with boundary layers in the background.