The design of a Control Maintenance system (CMs) for an airborne platform deeply deals with the mission, the on-board systems interfaces and the identification of their behaviour in operation. This paper describes how the Model Based Systems Engineering (MBSE) was applied to an industrial test case to perform the functional design of an innovative CMs to be integrated with the aircraft Fuel system (Fs). The impact of different approaches applied when modelling the two systems and their integration through the SysML was investigated. As the IBM Rational Rhapsody® tool was used, the Harmony® methodology was applied to the CMs, while a MBSE customized approach was implemented for the Fs, even to cope with some differences in coupling an avionic system to a physical one.