We demonstrated a new comprehensive method to combine scanning probe microscopy (SPM) nanolithography and modified SPM break junction techniques to fabricate and characterize single molecular break junction devices. By patterning alkanedithiol and alkanediamine molecules in the alkanethiol template and measuring the conductance of the two kinds of molecular junctions, we have shown the following: (1) the new "stretch-hold" approach produced four groups of conductance values for each molecular junction, for the first time realizing the less populated conductance values that correspond to different contact configurations; (2) the electronic transport mechanism for such molecular junctions is electronic tunneling with similar decay constants for each conductance group of the same kind of molecules. The conductance differences among different groups are due to the molecule-electrode contact configuration difference, which was shown by the extrapolated contact resistances. This new approach also allows one to eliminate, or at least minimize, the variations of experimental conditions and enables the measurement of multiple molecules under the same experiment with exactly the same experimental conditions.