Molecular doping is a method used to increase the charge carrier concentration within organic semiconductors to increase their conductivity. In an analogue to atomistic doping of inorganic semiconductors, in which an atom of the host material is replaced by an atom with one more or one fewer electron, molecular doping introduces larger molecules that react with the semiconducting backbone, typically by a redox reaction, which either introduces a hole or electron into the semiconducting system. A large class of organic semiconductors are conjugated polymers, which self-assemble into aggregate domains of higher order, where charge carriers can more easily hop interchain in their journey across the material. However, the analogue to atomistic doping breaks when considering the frequency of impurities: for efficient introduction of charge carriers, impurities are added in a ratio on the order of 10-3 to 10-6 to the host material, whereas molecular dopants, and hence impurities, are typically introduced on the order of 10-1. This high frequency of impurities disrupts features that lead to high mobility of charge carriers, such as polymer “tie” chains that connect domains of high mobility through domains of low mobility. There are methods that can minimize the damage of dopant to the underlying structure, such as the method of dopant introduction, as well as optimizing the amount of dopant to increase charge concentration without overwhelming the polymer with impurities. In Chapter 2, we study one such method of dopant introduction, vapor sequential doping, and how it introduces charge carriers while impacting the conjugated polymer structure, for the archetypical polymer-dopant pairing of poly(3-hexylthiophene-2,5-diyl) (P3HT) and 2,3,5,6-tetrafluoro-7,7,8,8-tetracyanoquinodimethane (F4TCNQ). We find that the aggregate domains of polymer are doped first and are responsible for the rapid rise in conductivity over six orders of magnitude, whereas the less mobile amorphous domains are doped second, and only increase the conductivity within an order of magnitude. In chapter 3, we investigate using weaker dopants with a similar chemical structure to F4TCNQ, and how changing the dopant strength changes the interplay between polymer structure and the vapor doping process. We find that the dopant strength in relation to the electron affinity of the aggregate and amorphous domains of the polymer determines whether the dopant is capable of effectively doping that domain, with our weakest dopant (TCNQ) not able to effectively dope either domain. Chapter 4 details a study using poly(3-(methoxyethoxyethoxymethyl)thiophene, which shares a backbone with P3HT but polar sidechains that allow for the solvation of ions for ionic transport. Using thermal treatments identified from the differential scanning calorimetry of this material, we see that we are able to control the local and long-range order both by the thermal treatment of the film as well as the addition of LiTFSI salt. Due to this material’s promise as a dual ionic and electronic conductor, we find that for this material that the best ionic and electronic conduction comes when the material is annealed just below its aggregate domain melting transition, leading to the largest aggregate domains with good alignment between the domains.