Over the last decade, the rise of the mobile internet and the usage of mobile devices has enabled ubiquitous traffic information. With the increased adoption of specific smartphone applications, the number of users of routing applications has become large enough to disrupt traffic flow patterns in a significant manner. Similarly, but at a slightly slower pace, novel services for freight transportation and city logistics improve the efficiency of goods transportation and change the use of road infrastructure. The present article provides a general four-layer framework for modeling these new trends. The main motivation behind the development is to provide a unifying formal system description that can at the same time encompass system physics (flow and motion of vehicles) as well as coordination strategies under various information and cooperation structures. To showcase the framework, we apply it to the specific challenge of modeling and analyzing the integration of routing applications in today's transportation systems. In this framework, at the lowest layer (flow dynamics) we distinguish app users from non-app users. A distributed parameter model based on a non-local partial differential equation is introduced and analyzed. The second layer incorporates connected services (e.g., routing) and other applications used to optimize the local performance of the system. As inputs to those applications, we propose a third layer introducing the incentive design and global objectives, which are typically varying over the day depending on road and weather conditions, external events etc. The high-level planning is handled on the fourth layer taking social long-term objectives into account.