Several wireless communication technologies, including Wireless Sensor Networks (WSNs), are essential for Internet of Things (IoT) applications. WSNs employ a layered framework to govern data exchanges between sender and recipient, which facilitates the establishment of rules and standards. However, in this conventional framework, network data sharing is limited to directly stacked layers, allowing manufacturers to develop proprietary protocols while impeding WSN optimization, such as energy consumption minimization, due to non-directly stacked layer effects on network performance. A Cross-Layer (CL) framework addresses implementation, modeling, and design challenges in IoT systems by allowing unrestricted data and parameter sharing between non-stacked layers. This holistic approach captures system dynamics, enabling network design optimization to address IoT network challenges. This paper introduces a novel CL modeling methodology for wireless communication systems, which is applied in two case studies to develop models for estimating energy consumption metrics, including node and network lifetime. Each case study validates the resulting model through experimental tests, demonstrating high accuracy with less than 3% error.