The morphology, optical properties, and photoconductance of blends of the poly(thienothiophene) derivatives poly(3,6-dialkylthieno[3,2-b]thiophene-co-bithiophene) (pATBT), poly(2,5-bis(3-alkylthiophen-2-yl)thieno[3,2-b]thiophene) (pBTTT), and poly(2,5-bis(3-dodecylthiophen-2-yl)thieno[2,3-b]thiophene) (pBTCT) with [6,6]-phenyl-C61-butyric acid methyl ester (PCBM) were studied. After thermal annealing, the pATBT:PCBM blend exhibits formation of phase-segregated polymer and PCBM domains. Annealing of pBTTT:PCBM and pBTCT:PCBM yields a layered structure with PCBM molecules intercalated between layers of π-stacked polymers. In the intercalated systems the photoluminescence is almost completely quenched, in contrast to the phase-segregated pATBT:PCBM blend. The higher degree of exciton quenching in the intercalated systems likely results in a higher initial yield of charges. However, on longer time scales (>10 ns), the microwave photoconductance for the layered systems is lower than for pATBT:PCBM blend systems. This is likely due to restricted motion of charges in intercalated systems, which reduces the yield of free charge carriers or enhances the charge carrier recombination.