The morphology of the active layer in polymer:fullerene solar cells is a key parameter for the performance. We compare bilayer poly(3-hexylthiophene)/[6,6]-phenyl-C61-butyric acid methyl ester (P3HT/PCBM) solar cell devices produced from orthogonal solvents before and after thermal annealing with P3HT:PCBM bulk heterojunction solar cells produced from a single solvent. By comparing the spectral shape and magnitude of the experimental and theoretically modeled EQEs we show that P3HT/PCBM bilayers made via orthogonal solution processing do not lead to bilayers with a sharp interface but that partial intermixing has occurred. Thermal annealing of these diffusive P3HT/PCBM bilayers leads to increased mixing but does not result in the same mixed bulk heterojunction morphology that is obtained when P3HT and PCBM are cast simultaneously from single solution. For thicker layers, the annealed bilayers significantly outperform the bulk heterojunction devices with the same nominal composition and same total thickness.