The Cahn-Hilliard equation is commonly used to study multi-component soft systems such as polymer blends at continuum scales. We first systematically explore various features of the equation system, which give rise to a deep connection between transport and thermodynamics-specifically that the Gibbs free energy of mixing function is central to formulating a well-posed model. Accordingly, we explore how thermodynamic models from three broad classes of approach (lattice-based, activity-based and perturbation methods) can be incorporated within the Cahn-Hilliard equation and examine how they impact the numerical solution for two model polymer blends, noting that although the analysis presented here is focused on binary mixtures, it is readily extensible to multi-component mixtures. It is observed that, although the predicted liquid-liquid interfacial tension is quite strongly affected, the choice of thermodynamic model has little influence on the development of the morphology.