Controlling the functioning of special equipment is the most important task both at the stage of prototyping and testing, and at the stage of operation. Functional control is understood as checking the electrical interaction of the systems of a special equipment product with each other in accordance with the relevant interaction protocols. At present, the improvement and development of new algorithms for the automated construction of control matrices of input and output signals, which, if necessary, change the logic of the electrical systems of the control object (changing the time of receiving or issuing electrical signals), will require minimal, nonresource-intensive adjustments during software debugging. is the most urgent technical problem in this topic. This article analyzes the control modes using a minimal set of initial data – the formation times of input and output electrical signals, which are completely determined by the protocols of interaction of control systems with the controlled object, and algorithms are determined that automatically generate control matrices of input and output signals. The presented block diagrams of algorithms allow you to form a zero control matrix, as well as determine the maximum key clock moment, using two mathematical matrices describing the input and output signals, while the interaction of special equipment product systems with external control systems at key clock moments is described by a transition graph. The proposed mathematical expression systems are adaptive in the event of serious changes in the operation of the systems of the object of control (or control systems), while the construction of algorithms according to the principles given in this article (the use of standard blocks performing specific tasks) will also make it easy to take into account the change in the form of the initial data. Regularities in the formation of input and output signals are revealed on the basis of the analysis of control over the functioning of various products of special equipment. If it is necessary to change the logic of the operation of the electrical systems of the controlled object (changing the time of receiving or issuing electrical signals), it is enough to correct the initial data, on the basis of which the control matrices of the input and output electrical signals will automatically change, which significantly reduces the software debugging time. Thus, the task of the developer of control modes is reduced to setting the minimum set of initial data – the times of formation of input and output electrical signals, which are completely determined by the protocols of interaction of control systems with the controlled object, then the developed algorithms allow automatically generating control matrices of input and output signals.