The continuous growth in data volume has sparked interest in silicon-organic-hybrid (SOH) nanophotonic devices integrated into silicon photonic integrated circuits (PICs). SOH devices offer improved speed and energy efficiency compared to silicon photonics devices. However, a comprehensive and accurate modeling methodology of SOH devices, such as modulators corroborating experimental results, is lacking. While some preliminary modeling approaches for SOH devices exist, their reliance on theoretical and numerical methodologies, along with a lack of compatibility with electronic design automation (EDA), hinders their seamless and rapid integration with silicon PICs. Here, we develop a phenomenological, building-block-based SOH PICs simulation methodology that spans from the physics to the system level, offering high accuracy, comprehensiveness, and EDA-style compatibility. Our model is also readily integrable and scalable, lending itself to the design of large-scale silicon PICs. Our proposed modeling methodology is agnostic and compatible with any photonics-electronics co-simulation software. We validate this methodology by comparing the characteristics of experimentally demonstrated SOH microring modulators (MRMs) and Mach Zehnder modulators with those obtained through simulation, demonstrating its ability to model various modulator topologies. We also show our methodology's ease and speed in modeling large-scale systems. As an illustrative example, we use our methodology to design and study a 3-channel SOH MRM-based wavelength-division (de)multiplexer, a widely used component in various applications, including neuromorphic computing, data center interconnects, communications, sensing, and switching networks. Our modeling approach is also compatible with other materials exhibiting the Pockels and Kerr effects. To our knowledge, this represents the first comprehensive physics-to-system-level EDA-compatible simulation methodology for SOH modulators.