NaxCoO2 has exceptional thermoelectric properties, including low thermal conductivity, and it is currently under consideration for use in power recovery applications and as a solid state refrigerator. Our neutron diffraction studies on SXD show that Na0.8CoO2 forms striped or square arrays of tri-vacancy clusters, depending on cooling rate. We have studied the phonon excitations in the striped phase using MERLIN, and the results are in agreement with first-principles DFT calculations. Our calculations for the square superstructure show that it will be much easier to observe the rattler mode responsible for the low thermal conductivity in this phase. We, therefore, propose to measure the phonon spectrum in the square phase by slow cooling to 200K. The results will provide a sensitive test of our calculations to optimize thermoelectric properties via patterning of superstructures.