Addressing the challenges the world is facing today demands a holistic approach. It is important not only to enhance individual pieces of the solution puzzle but also to grasp how they all interconnect. A paradigm shift is needed toward a systemic understanding, thus requiring the incorporation of a "system-of-systems" perspective. The complexity associated with such system-of-systems problems requires an equally holistic approach to be developed. Consequently, this work proposes a methodical step by step process for an efficient collaborative set-up of a complex system-of-systems model for overarching analysis and evaluation. This methodology is finally illustrated and explained using an application example of the European research project COLOSSUS focusing on creating novel solutions for advanced air mobility and wildfire fighting from a system-of-systems perspective.