Quantum Key Distribution (QKD) is an emerging cybersecurity technology that exploits the laws of quantum mechanics to generate unconditionally secure symmetric cryptographic keying material. The unique nature of QKD shows promise for high-security environments such as those found in banking, government, and the military. However, QKD systems often have implementation non-idealities that can negatively impact their performance and security. This article describes the development of a system-level model designed to study implementation non-idealities in commercially available decoy state enabled QKD systems. Specifically, this paper provides a detailed discussion of the decoy state protocol, its implementation, and its usage to detect sophisticated attacks, such as the photon number splitting attack. In addition, this work suggests an efficient and repeatable systems engineering methodology for understanding and studying communications protocols, architectures, operational configurations, and implementation tradeoffs in complex cyber systems.