The energy level alignment at the metal-organic and organic-organic interfaces of the Cu(100)/benzenethiolate/pentacene heterostructure is studied by photoemission spectroscopy and discussed theoretically using a model that includes, in a consistent way, charge transfer, Pauli repulsion, intrinsic molecular dipoles, and interface screening as a function of coverage. Despite the different nature of the two interfaces, our model provides a unified explanation for the work-function changes at both junctions and enables us to determine the benzenethiolate orientation as a function of coverage.