A key challenge in the field of organic electronics is predicting how chemical structure at the molecular scale determines nature and dynamics of excited states, as well as the macroscopic optoelectronic properties in thin film. Here, the donor–acceptor dyes 4,7-bis[5-[4-(3-ethylheptyl)-2,3-difluorophenyl]-2-thienyl]-2,1,3-benzothiadiazole (2,3-FFPTB) and 4,7-bis[5-[4-(3-ethylheptyl)-2,6-difluorophenyl]-2-thienyl]-2,1,3-benzothiadiazole (2,6-FFPTB) are synthesized, which only differ in the position of one fluorine substitution. It is observed that this variation in chemical structure does not influence the energetic position of the molecular frontier orbitals or the ultrafast dynamics on the FFPTB backbone. However, it does result in differences at the macroscale, specifically regarding structural and electrical properties of the FFPTB films. Both FFPTB molecules form crystalline films at room temperature, whereas 2,3-FFPTB has two ordered smectic phases at elevated temperatures, and 2,6-FFPTB does not display any liquid crystalline phases. It is demonstrated that the altered location of the fluorine substitution allows to control the electrostatic potential along the molecular backbone without impacting molecular energetics or ultrafast dynamics. Such a design strategy succeeds in controlling molecular interactions in liquid crystalline phase, and it is shown that the associated molecular order, or rather disorder, can be exploited to achieve ambipolar transport in FFPTB films.