Optimal thermal management is a key requirement in commercial utilization of lithium ion battery comprising of phase change electrodes. In order to facilitate design of battery packs, thermal management systems and fast charging profiles, a thermally coupled electrochemical model that takes into account the phase change phenomenon is required. In the present work, an electrochemical thermal model is proposed which includes the biphasic nature of phase change electrodes, such as lithium iron phosphate (LFP), via a generalized moving boundary model. The contribution of phase change to the heat released during the cell operation is modeled using an equivalent enthalpy approach. The heat released due to phase transformation is analyzed in comparison with other sources of heat such as reversible, irreversible and ohmic. Detailed study of the thermal behavior of the individual cell components with changing ambient temperature, rate of operation and heat transfer coefficient is carried out. Analysis of heat generation in the various regimes is used to develop cell design and operating guidelines. Further, different charging protocols are analyzed and a model based methodology is suggested to design an efficient quick charging protocol.