The Bifocal Modelling Framework (BMF) is an approach for science learning which links students' physical experimentation with computer modelling in real time, focusing on the comparison of the two media. In this paper, we explore how a Bifocal Modelling implementation supported learning outcomes related to both content and metamodeling knowledge, focusing on the role of designing models. Our study consisted of three conditions implemented with a total of 69 9th grade high-school students. The first and second classes were assigned two implementation modes of BMF: with and without a model design module. The third condition, employed as a control, consisted of a class that received instruction in the school's traditional approach. Our results indicate that students participating in both BMF implementations demonstrated improved content knowledge and a better understanding of metamodeling. However, only the 'BMF-with-design' group improved significantly in both content and metamodeling knowledge. Our qualitative analyses indicate that both BMF groups designed detailed models that included scientific explanations. However only students who engaged in the model design component: (1) completed a detailed model displaying molecular interaction; and (2) developed a critical perspective about models. We discuss the implications of those results for teaching scientific science concepts and metamodeling knowledge.