Self-assembly of molecular multilayers via metal ion linkages has become an important strategy for interfacial engineering of metalloid and metal oxide (MOx) substrates, with applications in numerous areas, including energy harvesting, catalysis, and chemical sensing. An important aspect for the rational design of these multilayers is knowledge of the molecular structure-function relationships. For example, in a multilayer composed of different chromophores in each layer, the molecular orientation of each layer, both relative to the adjacent layers and the substrate, influences the efficiency of vectorial energy and electron transfer. Here, we describe an approach using UV-vis attenuated total reflection (ATR) spectroscopy to determine the mean dipole tilt angle of chromophores in each layer in a metal ion-linked trilayer self-assembled on indium-tin oxide. To our knowledge, this is the first report demonstrating the measurement of the orientation of three different chromophores in a single assembly. The ATR approach allows the adsorption of each layer to be monitored in real-time, and any changes in the orientation of an underlying layer arising from the adsorption of an overlying layer can be detected. We also performed transient absorption spectroscopy to monitor interlayer energy transfer dynamics in order to relate structure to function. We found that near unity efficiency, sub-nanosecond energy transfer between the third and second layer was primarily dictated by the distance between the chromophores. Thus, in this case, the orientation had minimal impact at such proximity.