This chapter addresses the role of a conceptual representation, focusing on structure and mechanism, and models in scientific systems thinking. Conceptual representations are the big ideas in a domain that help organize knowledge and guide knowledge construction. Ecomodeler allows students to also capture and support their Explanations with Evidence (2E). The PMC-2E syntax is embedded in the modeling tool such that students and their teachers are aware that their model must consider these aspects of phenomena-mechanisms-components (PMC)-2E. The goal of research described in the chapter is to observe students' abilities to generalize their understanding of complex systems. To do so, the research draws upon two contrasting theoretical lenses of transfer (traditional analogical transfer and actor-oriented transfer) to shed light on students' abilities to transfer mechanistic reasoning skills and ideas about ecosystem processes within a technology-rich learning environment and use it solve new problems.