Heteroatom substitution is one promising way to favorably alter electronic transport in conductive polymers to improve their performance in thermoelectric devices. This study reports the spectroscopic, structural, and thermoelectric properties of poly (3-(3',7'-dimethyloctyl) chalcogenophenes) (P3RX) doped with 2, 3,5,7,8,, where the doping methodology, the heteroatom (X = Thiophene (T), Selenophene (Se), Tellurophene (Te)) and the extent of doping are systematically varied. Spectroscopic measurements reveal that while all P3RX polymers are appreciably doped, the doping mechanism is inherently different between the polymers. Poly(3-hexylthiophene) (P3HT, used in this study as a control) and P3RTe doped primarily via integer charge transfer (ICT), whereas P3RSe and P3RT appear to be doped via charge-transfer complex (CTC) mechanisms. Despite these differences, all polymers saturate with roughly the same number of F4TCNQ counterions (1 dopant per 4 to 6 heterocycles), reinforcing the idea that the extent of charge transfer from polymer to dopant varies significantly on the preferred doping mechanism. Grazing incidence wide-angle X-ray scattering measurements provide insight into the structural driving forces behind these different doping mechanisms -P3RT and P3RSe have similar microstructures in which F4TCNQ intercalates between the π-stacked backbones resulting in CTC doping (localized charge carriers), while P3HT and P3RTe have microstructures in which F4TCNQ intercalates in the alkyl-side chain region, giving rise to ICT doping (delocalized charge carriers). These structural and spectroscopic observations shed light on why P3HT and P3RTe