The effect of thin film morphology on energy transfer and migration in host-guest systems involving a phenylene-ethynylene oligomer matrix doped with colloidally prepared CdSe quantum dots is studied. Using correlated spectroscopy techniques including DSC, Raman, and temperature-dependent photoluminescence, we find that annealing the film produces continuous domain structures that enhance excitation migration by extending the excitation diffusion length. Under optical excitation, the thin films exhibit rapid melting of the host lattice, followed by resonant energy transfer to the CdSe QD guests. The ability to optically manipulate the structure and subsequently optically detect this change makes this material an important candidate for an all-optical read-write memory system.