The topic of the research is relevant, since the continuous search for effective systems and management instruments is a necessary condition for any economic operator to compete and develop. All successful companies in the world grow in this direction. The studies they carried out could be regarded as applied concepts of management theory producing tangible results which, however, cannot be effectively applied in all conditions and by any economic operator. The reasons why this happens determine the applicability of our research. The statement of the problem to be solved is as follows. The different results from the application of the same management methods could be explained by the fact that each company, firm, or corporation has its own unique structure and internal and external business environment. Moreover, an applied theory, being a concrete example of the respective fundamental one and therefore, having the same assumptions and provisions in principle, in fact may vary in some of them and even avoid them altogether. Our task is to construct methodological approaches to the development of applied management theories. To summarize, for the purpose of understanding what role the fundamental and the applied theories play in management, we have considered the general structure of a scientific theory as a system of knowledge and have shown that both the empirical basis and the use of knowledge in practical activities are an integral part of any theory. The conclusion we have reached to solve the problem stated is in offering a methodological approach to developing the theory of self-organization development for economic operators. The structure of the theory is presented in blocks with detailed descriptions and links between each of them.