<p>Understanding and controlling charge states at the level of individual electrons in molecular assemblies is often hindered by system complexity and the lack of reliable theoretical framework to accurately model the underlying many-body non-equilibrium electron dynamics. To address this challenge, here we construct well-defined molecular trimers and hexamers of tetrabromo-tetraazapyrene molecules by scanning probe manipulation and show that the electron dynamics can be completely rationalized using the Anderson impurity model and master equation approach. Our analysis demonstrates that such a treatment, which goes beyond the standard single-particle picture, is essential for understanding this class of molecular systems. The model not only quantitatively reproduces all features visible in measured differential conductance maps, but also uncovers the mechanism for negative differential conductance, which arises from the non-equilibrium occupancy of collective charge states. The analysis also reveals that the charging rings are not necessarily associated with changes in the total charge of the cluster, but often originate from internal charge rearrangements between the sites. These findings provide insight into fundamental quantum many-body effects in strongly interacting molecular systems and open pathways for engineering electronic phases by controlling cluster topology and the electrostatic environment.</p>