For many years, since Baars (1988) explicitly formulated it, contrastive analysis has been the key methodological approach in experimental studies of consciousness. When certain properly chosen psychological experimental setups (allowing an invariant target stimulus either to be consciusly experienced or not) were combined with brain-imaging methods, contrastive analysis became a quite powerful tool of research (Crick, 1994; Koch, 2004). By subtracting markers of brain processes recorded in the conditions without conscious experience of the target from the markers recorded in the conditions where the same target is consciously experienced it was believed that the markers of neural correlates of consciousness (NCC) can be obtained. However, as it turned out in the subsequent theoretical and experimental analysis, the picture is not so clear and simple (Bachmann, 2000, 2009; Miller, 2007; Aru et al., 2012; de Graaf et al., 2012). For example, when in the invariant conditions of independent variables a masked visual stimulus was consciously perceived or not (consciousness of the target standed as a dependent variable), NCC which were measured as a spectral perturbation of EEG was present already before stimulus presentation (Aru and Bachmann, 2009). Thus, the neural correlate of consciousness of a stimulus was present earlier than the stimulus itself was presented. Now, a reader must not get excited here because instead of some paranormal explanations brain-science based explanations can be comfortably used. In order to overcome the conceptual crisis hitting the traditional contrastive analysis based NCC research it was suggested that unconscious prerequisite processes (NCCpr) emerging as a result of contrastive analysis of brain-process markers of consciousness and similarly unconscious consequent processes (NCCco) must be differentiated from the constitutive processes directly associated with conscious experience (Aru et al., 2012; de Graaf et al., 2012). Thus, new experimental approaches were in need to avoid the trap of distilling prerequisite, direct, and consequent processes as mutually confounded and empirically inseparable. Despite some first attempts in this direction (Aru and Bachmann, 2015), the specialist landscape in this domain has remained obscure and no breakthrough solutions have been in sight. Moreover, there seems to be a number of additional uncertainties when we try to disentangle the various sub-types of NCC. Even NCCpr and NCCco are not unitary in terms of their theoretical meaning and associated neural processes. First, as the contents on which the perceptual report is founded can be selective, the markers of unused conscious contents may be erroneously neglected as markers of unconscious processes. They actually belong to consciousness level processes, but related to contents of consciousness qualitatively different from the ones specified by NCC. Second, in measuring NCC we must be able to disentangle contributions of the general consciousness enabling mechanisms and the selective contents representing mechanisms because their markers can be different and thus confused. In what follows I will substantiate these two issues.