To add a transition between two scenes in Synthesia:
Navigate to your video and select the scene you want to add a transition to.
Toggle the Scene transition on, located on the right-hand side of the canvas.
Select the style of transition for the scene from the list displayed.
Optionally - Click on Change All in the pop-up that appears after the selection to apply this scene transition to all scenes.
To add transition to other scenes in your video, select the scene you wish to add the transition to and repeat the process.