The properties of molecular films are determined by the geometric structure of the first layers near the interface. These are in contact with the substrate and feel the effect of the interfacial bonding, which particularly, for metal substrates, can be substantial. For the model system 3,4,9,10-perylenetetracarboxylic dianhydride on Ag(110), the geometric structure of the first monolayer can be modified by preparation parameters. This leads to significant differences in the electronic structure of the first layer. Here, we show that, by combining angle-resolved photoelectron spectroscopy with low-energy electron diffraction, we cannot only determine the electronic structure of the interfacial layer and the unit cell of the adsorbate superstructure, but also the arrangement of the molecules in the unit cell. Moreover, in bilayer films, we can distinguish the first from the second layer and, thus, study the formation of the second layer and its influence on the buried interface.