The connectivity between ordered domains in semiconducting polymers has been implicated as a bottleneck to charge transport. Crystallites in stiff-chain polymers have been shown to have ordered quasi-epitaxial domain boundaries using electron microscopy, but the factors affecting their formation have not been elucidated. A series of poly(benzo[1,2-b:4,5-b′]dithiophene-thieno[3,4-c]pyrrole-4,6-dione) (PBDTTPD) polymers with varying side chains were studied to determine the role of molecular structure on the formation of domain boundaries. Grazing incidence wide-angle X-ray scattering revealed the texture of ordered domains in these polymers as a function of thickness and thermal processing. High-resolution transmission electron microscopy (HRTEM) of thin films revealed that crystallites overlapped in an ordered fashion based on a geometric rule for the length of the crystallographic repeat length and the separation of the backbone by the side chains. All of the PBDTTPD polymers had polymorphic crystallites due to differences in alkyl stacking that behaved differently depending on their orientation to the substrate during thermal annealing. These results show the importance of domain orientation and boundaries on the morphology of semiconducting polymers.