Elements of the methodological basis of the theory of monitoring automated (computer-aided) systems structure-dynamics control are proposed in the paper. This theory can be widely used in practice. It has an interdisciplinary basis provided by the classic control theory, operations research, artificial intelligence, systems theory and systems analysis. The proposed approaches were implemented in software prototypes. The software prototypes were developed to simulate control processes for space-facilities control system (SF CS). The unified description of various control processes allows synthesizing both technical and functional structures of SF CS simultaneously. The presented multiple-model complex, as compared with known analogues, has several advantages. It simplifies decision-making in SF CS structure dynamics management, for it allows seeking for alternatives in finite dimensional spaces rather than in discrete ones. The complex permits to reduce dimensionality of SF CS structure-functional synthesis problems in a real-time operation mode.