Energy systems undergo several transformations, among them an increased integration of renewable energy sources, electric cars and heat pumps as well as an increased coupling of energy sectors. An approach using Cellular Energy Systems has gained popularity in research and discussions to control the challenges that emerge from these transformations by making even small flexibility available and planning and operating different energy sectors together. In this paper, a general methodology is proposed to handle flexibility in Cellular Energy Systems using flexibility models based on Affine Arithmetic.