Powertrain concepts incorporating renewable energies are an essential element of the energy revolution and increasingly require efficient manufacturing processes for electronic systems. Particularly, the joining of structures to be thermally coupled, such as the battery modules and the thermal management system (TMS), poses new challenges in process design. Factors that limit the process include the increased density, viscosity, and abrasiveness of thermal pastes as well as the pressure sensitivity of battery modules. The research presented aims to systematically investigate the influences of joining parameters on flow behavior, the formation of air inclusions, and the occurring joining forces to understand and systematically optimize the joining process. Employing a test setup following the Closing-Hele-Shaw-Cell, the influence of specific process parameters on the joining process such as the joining speed, joining gap, application pattern, and temperature was investigated for a silicone- and a polyurethane-based thermally conductive paste. The results indicate a high dependency of both the ensuing joining forces and the flow behavior on the parameters investigated. These insights imply a potential systematic parameter optimization and the specific adaptation of the joining process to improve flow behavior and reduce compressive stresses. This can ensure lower component deformations and qualify the process for the employment of cell types with a higher power density, a reduced encapsulation, and lower stiffness while at the same time improving production rates.