Unity allows you to use multiple scenes in your project. Multiple scenes can be useful when building HoloLens applications by putting the different states of the application in separate scenes. I use this a lot in my demo applications but also in applications for customers. Think of scanning the room in one scene while having the functionality placed in a second scene.
It is possible to set the active scene in Unity in the Hierarchy. By right mouse click on the scene you have the option called “Set Active Scene”. But this does not work when you deploy your scenes all together to Visual Studio.
To set the scene which needs to run at startup (active scene) you will need to go into the “Build Settings” dialog. Go to File > Build Settings… and make sure that the scene you want to have as startup scene is set at the top and has 0 indicated at the end. You can easily move scenes up and down by using the mouse.