Complex systems are challenging to design, particularly when they contain multi-level organizations with non-obvious relationships among design components. Here, we investigate engineering students’ capacity to search for optimal nanoscale biosystem designs with stochastic component and system behaviors. The study aims to characterize information types that facilitate human learning and improve their complex system understanding and design proficiency. It is hypothesized that learning parametric system relationships and/or inter-level causal mechanisms improves design proficiency; these relationships and mechanisms are teachable through software interfaces. Two contrasting learning/design interfaces were developed that presented differing information types: an interface with performance charts that emphasized parametric relationship learning and an interface with agent-based animations that emphasized inter-level causality learning. Users improved on pre-/post-learning design tasks with both interfaces; users who demonstrated inter-level causal relationship understanding, which occurred primarily with the animation interface, had greater improvement. All users were then presented contrasting animations of systems with opposing emergent behaviors, resulting in many more participants demonstrating an understanding of inter-level causal behaviors. These findings reveal the difficulties in understanding and designing multi-level systems and that interactive software tools may convey crucial information that supports engineering design, particularly with respect to the development of reasoning skills for how system components relate across levels.