I'm not aware of any temp files being stored while you are working...it does require user to perform save.
If session is connected to Windchill, you want to use Save annotations to store your annotation sets into the representation/annotation table in Windchill.
If not connected to Windchill, you still want to use Save annotations, but I have found that I have to use File Save As PVZ to create a new PVZ file to embed the annotations into the PVZ file. The File -> Save All function is flaky in Creo View so I don't recommend using this as your save button...or make sure that you are seeing the file time stamp get changed when you use this button.