This article provides an analysis on published models used to calculate phase separation in aqueous two-phase systems (ATPS) based on Flory-Huggins (FH) theory, in terms of problem formulation and mathematical solving algorithm. An integrated algorithm is presented, showing different mathematical approaches of using the FH theory. The algorithm involves the estimation of interchange energy, and the calculation of phase compositions. Based on experimental data, the thermodynamic model can provide a useful framework to perform a sensitivity analysis on parameters, in order to understand the influence of salt type, polymer molecular mass, and ionic strength on phase separation. However, this model, restricted to entropic and enthalpic terms, cannot quantitatively describe the data. This occurs mainly because of the strong influence of random experimental errors on the estimation of interchange energy and FH not being an exact description of phase separation in salt based ATPS. After providing a literature overview and mathematical analysis, we bring to the field the application of the FH theory for selecting ATPS and its limitations.