Integrated flow cell array (FCA) is an emerging technology, targeting the cooling and power delivery challenges of modern 2D/3D Multi-Processor Systems-on-Chip (MPSoCs). In FCA, electrolytic solutions are pumped through microchannels etched in the silicon of the chips, removing heat from the system, while, at the same time, generating power on-chip. In this work, we explore the impact of FCA system design on various 3D architectures and propose a methodology to optimize a 3D MPSoC with integrated FCA to run a given workload in the most energy-efficient way. Our results show that an optimized configuration can save up to 50% energy with respect to sub-optimal 3D MPSoC configurations.