Quantum transport through single molecules is very sensitive to the strength of the molecule-electrode contact. Here, we investigate the behavior of a model molecular junction weakly coupled to external electrodes in the case where charging effects do play an important role (Coulomb blockade regime). As a minimal model, we consider a molecular junction with two spatially separated donor and acceptor sites. Depending on their mutual coupling to the electrodes, the resulting transport observables show well defined features such as rectification effects in the I-V characteristics and nesting of the stability diagrams. To be able to accomplish these results, we have developed a theory which allows us to explore the charging regime via the nonequilibrium Green function formalism, and found full agreement with the master-equation results. Our theory, beyond its experimental relevance, offers a transparent framework for the systematic and modular inclusion of a richer physical phenomenology.