The self-assembly and electron transfer properties of adsorbed organic molecules are of interest for the construction of miniaturized molecular circuitries. We have investigated with scanning probe microscopy the self-organization of two structurally related molecular wires embedded within a supportive alkanethiol matrix. Our results evidence heterogeneous adsorption patterns of the molecular wires on gold with either incommensurate unit cells driven into assembly by lateral interactions or a dynamic, commensurate distribution on gold, along with formation of distinct 2D phases. We also observed diffusion-based conductance switching for one of the molecular wires, due to its propensity toward weaker lateral interactions and Au-S adatom formation. We have further demonstrated through the use of scanning tunneling spectroscopy differential current-voltage response for each molecular wire, despite their close structural similarity. Such molecular wires embedded in alkanethiol matrix and exhibiting conductance-switching phenomena have the potential to be used for the functionalization of electrodes in bioelectronic devices.