Theoretical studies of charge transport in organic conducting systems pose a unique challenge since they must describe both extremely short-ranged and fast processes (charge tunneling) and extremely long-ranged and slow ones (molecular ordering). The description of the mobility of electrons and holes in the hopping regime relies on the determination of intermolecular hopping rates in large-scale morphologies. Using Marcus theory these rates can be calculated from intermolecular transfer integrals and on-site energies. Here we present a detailed computational study on the accuracy and efficiency of density-functional theory based approaches to the determination of intermolecular transfer integrals. First, it is demonstrated how these can be obtained from quantum-chemistry calculations by forming the expectation value of a dimer Fock operator with frontier orbitals of two neighboring monomers based on a projective approach. We then consider the prototypical example of one pair out of a larger morphology of tris(8-hydroxyquinolinato)aluminium (Alq(3)) and study the influence of computational parameters, e.g. the choice of basis sets, exchange-correlation functional, and convergence criteria, on the calculated transfer integrals. The respective results are compared in order to derive an optimal strategy for future simulations based on the full morphology.