Three isomeric π-conjugated molecules based on diketopyrrolopyrrole and bithiophene (DPP2T) substituted with hexyl side chains in different positions are investigated for use in solution-processed organic solar cells. Efficiencies greater than 3% are obtained when a mild annealing step is used. The position of the side chains on the DDP2Ts has a major influence on the optical and electronic properties of these molecules in thin semicrystalline films. By combining optical absorption and fluorescence spectroscopy, with microscopy (AFM and TEM) and scattering techniques (GIWAXS and electron diffraction), we find that the position of the side chains also affects the morphology and crystallization of these DPP2Ts when they are combined with a C70 fullerene derivative in a thin film. The study demonstrates that changing the side chain position is an additional, yet complex, tool to influence behavior of conjugated molecules in organic solar cells.