Doping of thin films of semiconducting polymers provides control of their electrical conductivity and thermopower. The electrical conductivity of semiconducting polymers rises nonlinearly with the carrier concentration, and there is a lack of understanding of the detailed factors that lead to this behavior. We report a study of the morphological effects of doping on the electrical conductivity of poly(3-hexylthiophene) (P3HT) thin films doped with small molecule 2,3,5,6-tetrafluoro-7,7,8,8-tetracyanoquinodimethane (F4TCNQ). Resonant soft X-ray scattering shows that the morphology of films of P3HT is not strongly changed by infiltration of F4TCNQ from the vapor phase. We show that the local ordering of P3HT, the texture and form factor of crystallites, and the long-range connectivity of crystalline domains contribute to the electrical conductivity in thin films. The thermopower of films of P3HT doped with F4TCNQ from the vapor phase is not strongly enhanced relative to films doped from solution, but the electrical conductivity is significantly higher, improving the thermoelectric power factor.