Internet satellite constellations are expected to play an important role in accommodating the rising global demand for internet access. Such rise in demand, however, is highly uncertain. Staged deployment is an approach that provides flexibility to tackle demand uncertainty by enabling the real option to reconfigure a constellation if demand changes. Advancements in satellite technology have led to the emergence of multi-layered constellations. This opens the opportunity to enhance staged deployment by enabling an additional real option: adding a new layer to a constellation. This real option has no associated reconfiguration costs, and therefore has the potential to reduce the cost of staged systems deployment. This paper proposes a framework to design multi-layer staged deployment systems and analyse their effectiveness in modern mega-constellations under global demand uncertainty. The framework is applied to four case studies based on market projections. Results show that multi-layer staged deployment decreases the expected life-cycle cost (ELCC) by 42.8% compared to optimal traditional single-layer deployment. Multi-layer staged deployment is more cost effective than single-layer staged deployment in all practical cases, which decreases ELCC by 22.9% compared to traditional deployment. Several cost altering mechanisms in staged deployment are identified. The results and analysis provide improved economic performance and better resource utilization, thus contributing in the long term to improved sustainability and market resilience. An accompanying decision support system provides system engineers with valuable insights on how to reduce deployment costs using the proposed multi-layered staged strategy.