Due to the multidisciplinary character of psychophysiology, the problem of comparability of psychological and physiological phenomena of different natures and levels of organization has always been raised. This requires the interaction of theory and methodology to appropriately address the specifics of the psychophysiological paradigm, all the while maintaining their grounding in the actual psychological and physiological concepts. The history of EEG studies of mental activity shows that a weak theoretical basis at certain stages can result not only in methodological crises but can also affect empirical data collection and interpretation. An adequate theory can lend strong support to the methodology with "brain-oriented" structuring of psychological tasks and such a theory improves the neurophysiological informative value of the EEG parameters referring to the psychological characteristics of mental processes etc. On the other hand, the great importance of the EEG recording and processing techniques can result in overrating technological progress, hence frequently holding back meaningful interpretation and construction of a comprehensive psychophysiological conceptual framework. This in turn causes demands for higher material and intellectual outlays, due to overspecialization in research, and results in work duplication as well as the creation of a fragmentary knowledge structure. This article illustrates how the multidisciplinary interaction of theory and methodology, when focused on theoretical problems, can yield a series of concepts with escalating levels of integration, bringing together such different branches of psychophysiology as the study of functional states and of individual differences. As a result, this extends the theoretical model based on normal material to encompass borderline constitutional psychopathology.