When you scan an upper arch and a lower arch with an intra-oral scanner and then export that case, usually the software places coordinates on the upper and lower models, so when you import them into another software, they properly articulate.
In this video, you can see how the upper arch is stitched to the CT image of the maxilla, an then how one can easily related the mandible stl file to articulate to the upper arch. This comes in handy in software like BlueSkyBio where you could add teeth to the equation and design implants so that they are prosthetically driven during the design phase.
In this video, you can see how a quadrant of the lower arch and the upper arch can be imported into a third party software for design. Note that in this particular demonstration, there is not edentulous area and this video just demonstrates how you can place a digital tooth in your case and design the digital wax up to your liking. Advanced users generally just use the sleeve of the surgical stent to aid them in visualizing the occlusal table of the final prosthesis. A complete design lets you know where the contacts are and how much space you need to create the proper emergence profile.