You can use hosted feature layers, tile layers, scene layers, elevation layers, map image layers and vector tile layers in the Scene Viewer. When you are logged into your account you will see an edit pencil in the top left hand corner which allows you to add layers into the scene viewer that exist in ArcGIS Online or you can add them from your server through URL.
Feature collections like map notes, shapefiles and csv layers are currently not supported in the Scene Viewer.
Let me know if you have any other questions.
Russ