The modeling of stacking machines for battery cell production offers potentials for quantifying interdependencies and thus optimizing development and commissioning processes against the background of a targeted efficient production. This paper presents a methodology to develop a model for quantifying machine-side influences using the example of a Z-Folding machine. The components and aspects of the machine to be modeled and their level of detail are systematically derived. Subsequently, it is shown how to parameterize the derived aspects. The components and aspects of the machine are modeled and connected through a multi-physics simulation. This makes it possible to predict the effects on the separator material to be processed depending on the selected setting parameters on the machine. This opens up potentials, for example, to identify optimal setting parameters in a risk-free and model-based manner, depending on the materials to be processed. As a result, material waste can be reduced by eliminating previous "trial and error" approaches.