This work shows that given the numerous specific constraints that PHM systems for turbofan engines have to deal with and despite the low level of criticality of such systems, the use of Systems Engineering (or even System of Systems Engineering) methods and tools is essential to ensure project success. Various aspects of the methodology which were applied in our projects are presented here: on one hand general system design and project management considerations, on the other hand transversal methodological items such as model-based systems engineering and methods to manage requirements, hypotheses, interfaces, configuration, change, compatibility, validation, verification and integration. Associated pitfalls and lessons learned from applying these elements are highlighted, especially the importance of defining from the beginning of the design all the project management plans, with a constant focus on customer needs satisfaction, interfaces and design documentation while allowing iterations.