Well the fade overlay will always be on top, so there is no issue just setting it to like 500 if you want. Also, you can script the layer index, for example, if you have a container that has CanvasLayers as children, you can iterate through all the children and set their index 1 by 1.
But honestly, if you have more than a couple CanvasLayers in your game, you're probably doing something wrong. There is really no need for more than 2 or 3, so if you have a bunch there is a problem in your design. And if there are only 3, just set the indices manually as that is the simplest thing.