[Karrot_Kream]

I really enjoyed "Business Dynamics: Thinking and Modelling for a Complex World" by John Sterman. It's an older book, but it answers all of the questions that you ask. The book starts out by giving a high level overview of how systems modelling (and iteration on these models) occurs in practice, along with case studies and models that represent those case studies. The book talks about stocks and flows and real life examples on how stocks and flows work. While I wouldn't say this book is as rigorous as an engineering math text, it has a section on nonlinear dynamical systems and the math that these models represent in some sparse detail, so you can try to apply rigor to the models presented.