In weakly interacting organic semiconductors, static and dynamic disorder often have an important impact on transport properties. Describing charge transport in these systems requires an approach that correctly takes structural and electronic fluctuations into account. Here, we present a multiscale method based on a combination of molecular dynamics simulations, electronic structure calculations, and a transport theory that uses time-dependent non-equilibrium Green's functions. We apply the methodology to investigate the charge transport in C$_{60}$-containing self-assembled monolayers (SAMs), which are used in organic field-effect transistors.