We present the results of investigations aimed at understanding the mechanisms by which small, mutually immiscible organic molecules self-assemble into domains during phase separation from liquid solutions in the presence of a solid substrate. As an example system, we investigated molecular mixtures of tetranitro zinc-phthalocyanine (tn-ZnPc), an electron donor, and [6,6]-phenyl-C61-butyric acid methyl ester (PCBM), an electron acceptor, in chloroform solution, deposited onto native oxide-covered Si(111) substrates. We found qualitatively different behavior in the formation of domains of the two types of molecules, seemingly because of a large difference in their solubilities in the solvent. The morphology of PCBM molecule domains varies widely depending on the solvent evaporation rate, the presence/absence of tn-ZnPc molecules in the solution, solvent annealing conditions, and seemingly the presence/absence of trace impurities. By contrast, we find evidence that the shape of the tn-ZnPc domains is insensitive to evaporation; these form while in liquid suspension, and the assembly of domains into clusters varies according to the rate and mode of solvent evaporation.