<p>This article is the second part of the study, which proposes a methodology for mathematical modeling of the phased development of nodes and transport routes in a hierarchical network with multicommodity discrete correspondence flows. As a rule, such networks consist of a decentralized mainline network and networks in the internal service areas of mainline nodes. In a multicommodity network, each node can exchange correspondence (products, goods, cargo, messages) with others. In the mainline network, all correspondence is transmitted via communication channels or transported by vehicles in transport units of a specified size (capacity, volume). In this part of the study, using the example of transportation networks, it is experimentally shown that the step-by-step solution to the problems of optimizing the structure of the mainline network and the distribution and routing of flows allows obtaining initial data for constructing dynamic deterministic and stochastic models of their development. The authors also demonstrated how one can use these problems for the operational redistribution of flows in case of equipment failures in nodes and communication lines (exceeding the capacities of nodes and communication channels, the transportation capacity of vehicles, etc.).</p>