By using scanning tunneling microscopy (STM), we studied the heteroleptic double-decker complex TbNPcPc (NPc = naphthalocyaninato and Pc = phthalocyaninato), where two different planar ligands sandwich a Tb(III) ion and an unpaired π electron causes Kondo resonance upon adsorption on the Au(111) surface. Kondo resonance is a good conductance control mechanism originating from interactions between conduction electrons and a localized spin. Two types of adsorption geometries appear depending on which side contacts the substrate surface, which we call Pc-up and NPc-up molecules. They make intriguing molecular assemblies by segregation. In addition, different adsorption geometries and molecular assemblies provide a variety of spin and electronic configurations. Pc-up and NPc-up molecules both showed the Kondo resonance when they were isolated from other molecules, but their Kondo temperatures were different. A one-dimensional chain composed of only NPc-up molecules was found, in which the dI/dV plot showed a conversion from the Kondo peak to a dip at the Fermi energy. In addition, a two-dimensional lattice with an ordering of Pc-up and NPc-up molecules in an alternative manner was observed, in which no Kondo peak was detected in the molecule. The absence of the Kondo peak was accounted for by the change of azimuthal rotational angle of the two ligands of both molecules. The results imply that a molecule design and adsorption configuration tailoring can be used for the spin-mediated control of the electronic conductance of the molecule.