Layers in the transition designer can't be sorted within their screen as they can in the canvas overview. However, you can move layers to three positions outside of their current screen.

Pulling layers out of their screens helps when you need to modify the stacking order of layers in a transition.

To Pull Out a Layer Click a layer in the layer list of the Transition Designer and drag it to the top, bottom or middle of the layer list. The middle section is between the two screens.