We investigate the way students' reasoning about evolution can be supported by drawing-based modeling. We modified the drawing-based modeling tool SimSketch to allow for modeling evolutionary processes. In three iterations of development and testing, students in lower secondary education worked on creating an evolutionary model. After each iteration, the user interface and instructions were adjusted based on students' remarks and the teacher's observations. Students' conversations were analyzed on reasoning complexity as a measurement of efficacy of the modeling tool and the instructions. These findings were also used to compose a set of recommendations for teachers and curriculum designers for using and constructing models in the classroom. Our findings suggest that to stimulate scientific reasoning in students working with a drawing-based modeling, tool instruction about the tool and the domain should be integrated. In creating models, a sufficient level of scaffolding is necessary. Without appropriate scaffolds, students are not able to create the model. With scaffolding that is too high, students may show reasoning that incorrectly assigns external causes to behavior in the model.