Uncertainty is present in model-based developments in many different ways. In the context of composing model-based analysis tools, this chapter discusses how the combination of different models can increase or decrease the overall uncertainty. It explores how such uncertainty could be more explicitly addressed and systematically managed, with the goal of defining a conceptual framework to deal with and manage it. We proceed towards this goal both with a theoretical reasoning and a practical application through an example of designing a peer-to-peer file-sharing protocol. We distinguish two main steps: (i) software system modelling and (ii) model-based performance analysis by highlighting the challenges related to the awareness that model-based development in software engineering needs to coexist with uncertainty. This core chapter addresses Challenge 5 introduced in Chap. 3 of this book (living with uncertainty).