This tutorial describes methodologies to model and understand the collective behavior or different types of urban systems. It highlights under what physical properties the aggregated laws will provide reasonable description of congestion for single- and multi-modal systems. Ultimately, the goal is to develop optimization tools and investigate what type of real-time active traffic management schemes (congestion pricing, vehicle restriction, large scale traffic signal control) can improve mobility measures in a city for cities of different structures. A hierarchical feedback control network of multiple levels is analyzed. The validation of the modeling methodologies and the traffic management schemes are conducted in various and complex city structures scenarios using data from field experiments and micro-simulations.