Hello,
I am not a specialist of netcdf, but I can suggest an idea. To add special libraries, you can do like in the example of file systel-all.ini in the config directory (see svn repository) for MED or HDF5. See the lines
#IF MED AND HDF5
#MED LK_OPT_NORMAL=" -lf2c -lz -lstdc++ -v "
#MED LK_LIB_SPECIAL="-L/home/systel/LIBRARY/MED/med_2.3.4_intel_64_10/lib -lmed -L/home/systel/LIBRARY/HDF5/hdf5_1.6.4_intel_64_10/lib -lhdf5 "
Maybe with the variable LK_LIB_SPECIAL="-L/export/apps/netcdf4/lib/ -lnetcdf -lnetcdff" you can reach your goal. Please try it and tell me. Do not forget after changing your "systel.ini" file to type cfgmak in the same directory to update the file cfgmak.mak so that your makefiles are coherents with your options to compile.
Hope this helps,
Chi-Tuan