This paper discusses elements of the theory of conceptual-innovation and energy-resource management based on the system concept of technologically innovative providing of resource synergistic transport integration of a discontinuous terminal infrastructure of a transport system (TS) in accordance with transport demand and the systemic requirement of an innovative increase in the energy-resource quality of transportation services (ERQTS). It has been established that for the system enhancement of ERQTS are actual the development of innovation management theory and the implementation of conceptual improvement strategies for a number of subsystem and system factors: transport resources and technical properties, transport technologies, as well as innovative reproduction functions of the motor transport subsystem (MT) and integrative-equifinal functions of the motor transport system (MTS). The existing theory of service commercial management in MT is based on a simplified non-production and empirically conservative paradigm of knowledge about MT as a sphere of transport services (without product description) , therefore it does not fundamentally correspond to the above-mentioned concept of development of MTS and MT. This theory uses computational schemes for virtual transportation and service past costs, so it is non-innovative and technologically degenerate. A theory of conceptual and technologically innovative improvement of ERQTS, as well as the functions of MT and MTS, has been developed. A comprehensive model of the target function of the system-conceptual management of ERQTS is proposed, taking into account the improvement of the MTS and MT functions according to the principle of energy-resource synergy in the transport services life cycle. It takes into account: ways to eliminate the paradoxical fragmentation of types of knowledge about transport operations and processes, improving the properties of a car as a resource-technical means of transport production and reproduction, the essence of transport operations and technologies, as well as dysfunctions of subsystems of MTS.