Organic solar cells based on the combination of squaraine dyes (as electron donors) and fullerenes (as electron acceptors) have recently garnered much attention. Here, molecular dynamics simulations are carried out to investigate the evolution of a squaraine-C60 bilayer interface as a function of the orientation and order of the underlying squaraine layer. Electronic couplings between the main electronic states involved in exciton dissociation and charge (polaron pair) recombination are derived for donor-acceptor complexes extracted from the simulations. The results of the combined molecular-dynamics-quantum-mechanics approach provide insight into how the degree of molecular order and the dynamics at the interface impact the key processes involved in the photovoltaic effect.