The problems of managing modern complex organizational and manufacturing systems, such as international production corporations, regional economies, sectoral ministries, etc., in conditions of fierce competition are primarily related to the need to consider the activity of organizational and manufacturing objects that make up a multi-level manufacturing system, that is, the ability to efficiently solve the problem of coordinating interests. This problem cannot be solved efficiently without the use of modern scientific achievements and appropriate software. As an example, we can cite the active systems theory pioneered by Prof. V. M. Burkov and his students, which successfully claims to be a constructive implementation of the idea of coordinated planning. This paper proposes new models and methods of coordinated planning of two-level organizational and manufacturing systems. Our models and methods use original compromise criteria and the corresponding constructive algorithms. The original aggregated volume-time models are used as models of organizational and manufacturing objects. We present a well-founded software structure for the proposed methods of coordinated planning. It contains an intelligent interface for using the presented results in solving applied problems.