Many energy systems require control frameworks that can manage dynamics spanning multiple timescales and can make decisions for both continuous and discrete inputs. This paper meets this need for a class of switched power flow systems modeled using graphs. Conditions are provided under which each mode of these models belongs to the class of cooperative systems. Leveraging properties of cooperative systems, a two-level hierarchical control framework is constructed in which an upper level controller governs slow dynamics to plan for long-term future behavior and select modes, while a lower level controller governs fast dynamics to improve performance and reject disturbances. The control framework guarantees satisfaction of state constraints while also ensuring that a minimum bound on the rate of energy transfer to the system can always be achieved. The applicability and efficacy of the approach is demonstrated in simulation on a fluid-thermal system representative of those found in aircraft.