We use a systematic approach that combines experimental X-ray diffraction (XRD) and computational modeling based on molecular mechanics and two-dimensional XRD simulations to develop a detailed model of the molecular-scale packing structure of poly(2,5-bis (3-tetradecylthiophene-2-yl)thieno[3,2-b]thiophene) (PBTTT-C-14) films. Both uniaxially and biaxially aligned films are used in this comparison and lead to an improved understanding of the molecular-scale orientation and crystal structure. We then examine how individual polymer components (i.e., conjugated backbone and alkyl side chains) contribute to the complete diffraction pattern, and how modest changes to a particular component orientation (e.g., backbone or side-chain tilt) influence the diffraction pattern. The effects on the polymer crystal structure of varying the alkyl side-chain length from C-12 to C-14 and C-16 are also studied. The accurate determination of the three-dimensional polymer structure allows us to examine the PBTTT electronic band structure and intermolecular electronic couplings (transfer integrals) as a function of alkyl side-chain length. This combination of theoretical and experimental techniques proves to be an important tool to help establish the relationship between the structural and electronic properties of polymer thin films.