Learners' use of digital simulations is an important dimension of scientific modeling. Prior studies show teachers may misconstrue the epistemic affordances of simulation, valuing simulations for their ease of use to portray information (Bo et al. "Journal of Science Education and Technology," 27, 550-565, 2018) and for their aesthetic features (Schwarz et al. "Journal of Science Teacher Education," 18(2), 243-269, 2007). Teachers' development of more sophisticated epistemologies of simulation as sensemaking and problem-solving tools may better inform their pedagogical decisions, including teachers' critical selection of simulations, deciding when to introduce them within the curriculum, and how to elicit students' critique of the simulations. These considerations position simulations as "knowledge-building" tools within modeling practice, rather than demonstrations of final-form facts. To this end, this study examines preservice teachers' (PSTs') work in a semester-long introductory engineering and physical science course in which preservice teachers regularly used and critically reflected on educational simulations. We employ thematic analysis to describe their evolving epistemologies of simulation as learning tools in science and engineering contexts. Drawing on scholarship concerning learners' epistemic agency and scientists' participation in a dialectical exchange of agency between themselves and the scientific tools they use, we demonstrate that PSTs increasingly (1) recognized key sensemaking affordances of digital simulations used for science learning and design, (2) attend to tools' resistance (Pickering, 1995) to comply with the PSTs' intentions as a productive part of scientific practice, and finally (3) acknowledge their own and learners' agency in relation to simulation practices. We also describe the pedagogy that deepened learners' understanding of the nature of simulation practices in science and engineering contexts.