Effect of dynamics of site energy disorder on charge transport in organic molecular semiconductors is not yet well-established. In order to study the relationship between the dynamics of site energy disorder and charge transport, we have performed a multiscale study on dialkyl substituted thienothiophene capped benzobisthiazole (BDHTT-BBT) and methyl-substituted dicyanovinyl-capped quinquethiophene (DCV5T-Me) molecular solids. In this study, we explore the structural dynamics and correlated charge transport by electronic structure calculations, molecular dynamics, and kinetic Monte-Carlo simulations. We have also proposed the differential entropy dependent diffusion and charge density equations to study the electric field drifted diffusion property and carrier density. In this investigation, we have addressed the transformation mechanism from dynamic to static disorder in the extended stacked molecular units. Here, the decrease in the charge transfer rate due to site energy fluctuations reveals the dispersion transport along the extended π-stacked molecules. Furthermore, the calculated current density for a different set of site energy difference values shows the validity and the limitations of the Einstein relation. Based on the calculated ideality factor, we have classified the charge transport in these molecules as either the Langevin or the Shockley-Read-Hall type mechanism. Through the calculated mobility, current density, and ideality factor analysis, we categorize the applicability of molecules of interest for photovoltaic or light emitting diode applications.