Structure-property relationships associated with a hybrid siloxane-terminated hexyl chain (SiC6), molecular packing, thin-film morphology, and charge carrier transport are reported for two new naphthalene diimide (NDI)-based polymers; P(NDI2SiC6-T2) consists of NDI and bithiophene (T2) repeating units, while for P(NDI2SiC6-TVT), the (E)-2-(2-(thiophen-2-yl)-vinyl)thiophene (TVT) units are introduced into the NDI-based backbone. The analysis of the optical spectra shows that the pre-aggregation of these polymers in solution is highly sensitive to the choice of solvent. The polymer films cast as a coating from chloroform (CF) favor a mixed crystalline orientation, while 1-chloronaphthalene (CN)-cast films favor an almost edge-on orientation, resulting in a difference in mobility. Within this work, the annealed P(NDI2SiC6-T2) device fabricated from CF, despite showing a less densely packed organization, shows the highest electron mobility due to a highly balanced crystalline orientation.