There are different ways of showing a layer. You can have them open as in a tabbed interaction where the base layer needs to be clicked on. In these instances you need to ensure the objects in your layers are directly after the button in the focus order that shows that layer in a logical order.
The other way is when you show a popup and the base layer cannot be clicked in these cases you can set them to either a dialogue layer or set them to prevent the user clicking on the base layer and in this situations you only need to set the focus order for each layer to be logical as they will automatically take focus so you don’t need to move the objects in the focus order.
Sent from my iPhone