This tutorial presents a practical technique for managing the architecture of software product lines using inter-module dependencies. We will show that the Lightweight Dependency Model approach, based on dependency structure matrices, is highly scalable compared to the directed graph approaches that are common today. We will also show a variety of matrix algorithms and transformations that can be applied to analyze and organize the system into a form that reflects the architecture and demonstrates the importance of managing dependencies in product lines. We illustrate our approach by applying it to real applications each consisting of hundreds or thousands of files. We will show how dependency models can be created for product lines and how formal design rules can be specified to manage the evolution of these architectures.