The choice of dopant and the method used to introduce a dopant can greatly influence the resulting electronic and thermoelectric properties of conjugated polymers. Multiple factors contribute to these dopant dependent properties; including how the dopant affects the polymer crystallinity and film morphology, how close the dopant molecule is to the pi-conjugated backbone, and how efficiently the dopant creates polarons on the polymer. In this work we investigate the influence of large molybdenum complexes as dopants vs. smaller iron complexes on the electrical conductivity and Seebeck coefficient of several conjugated polymers. For multiple polymers we find that the large molybdenum complexes lead to electrical conductivities that are over an order of magnitude higher than that of the iron complexes at low doping concentrations. However, the electrical conductivity of the polymers doped with the molybdenum complexes saturate at much lower doping concentrations than the iron complexes. Thus, the iron complexes can lead to overall greater electrical conductivities and higher power factors than the molybdenum complexes. Through grazing incidence X-ray diffraction measurements and optical spectroscopies, we find that a major reason for the large differences in the electrical conductivities of the polymers doped with the molybdenum and iron complexes is due to significantly different effects on the film morphologies.