Alkyl chains are often attached to the periphery of semiconductor molecules to impart solubility and they represent a pervasive structural element in solution processable, organic photovoltaics (OPV). It is important to understand the effects of such substitutions on the morphology and performance of organic solar cells. This investigation focuses on determining structure-property correlations in OPV devices constructed with small-molecule, solution processable electron donors based on benzothiadiazole-dithienopyrrole, mixed with the electron acceptor PCBM. Two donor molecules with the same opto-electronic molecular properties but differing alkyl substituents - without (BD) or with (BD6) hexyl side chains - are studied. The resulting device data for fabricated solar cells, across a range of processing conditions, is compared to thin-film morphology, spectroscopy, thermal analysis, and molecular dynamics simulations. Two device states of higher and lower performance, depending on the casting solvent, are obtained for the molecule without the side chains (BD); both states have amorphous mesoscale structure, but show subtle differences in the nanoscale phase separation. In contrast, for the molecule with side chains (BD6) devices have highly variable reproducibility and middling efficiency and photocurrent. The BD6 donor exhibits lower miscibility with PCBM, which correlates with the formation of a donor-enriched layer on the surface of the solar cell.