Certain phase retrieval methods use knowledge about the free space propagation of a wave to phase a paraxial beam passing through one or more measurement planes. This approach has been widely applied and has been shown to quantitatively retrieve the refractive index profile of a sample. The quality of the phase retrieval will depend on a range of factors including sample feature size, propagation distance, measurement plane separation, wavelength and noise. Here we describe an optimisation study for two-plane phase retrieval using a laboratory-based X-ray source that considers all of these factors. We discuss our results in the context of a three-dimensional reconstruction of a sample refractive index profile.