New nano-scale electronic devices past the Silicon era based on two-dimensional (2D) materials bear the promise of providing small, better performing devices. However the confined geometries in e.g. transistors, that make possible the small scale also poses a thermal management problem due to resistive heating during operation. For a device based on a 2D material where the heat is generated in the plane such as a transistor based on Molybdenum disulfide, most of the heat is removed out of the plane and into the substrate, typically Silicon dioxide, and is limited by the thermal boundary conductance (TBC) associated with the interfaces of the 2D material with the surrounding materials. Knowing the TBC of the 2D material with the surrounding materials is key to successfully designing a fully operational next generation nano electronic device. However, experimental values for the TBC of Molybdenum disulfide with Silicon dioxide varies over an order of magnitude and the details of what each interface contributes to the overall thermal conductance of the system are not accessible directly from experiments. Here, a molecular dynamics simulation study is presented that looks at the heat transport in a system with Molybdenum disulfide stacked between a Silicon dioxide substrate and a covering metal (Titanium). A system without Molybdenum disulfide is also investigated and the two systems are compared to experimental values. In addition, systems with only one of the interfaces, Molybdenum disulfide-Silicon dioxide or Titanium-Molybdenum disulfide, are also studied and used to assess the effect of stacking the 2D material on the TBC. The results show that the TBC of the single interface systems can not predict what the TBC would be in the stacked system and that the TBC is increased for both interfaces in the stacked system compared to the single interface systems.