By default, the Order toolbar contains quick access tools for controlling the relative position of overlapping markups. These tools can be used on one or more markups. These tools are unavailable/dimmed when no markup is selected. The same tools can also be accessed by right-clicking a markup and going to Order.
If the toolbar is currently hidden, go to View > 
Toolbars and select it to show it.
Bring to Front (CTRL+SHIFT+]): Moves the selected markup in front of any other overlapping annotations.
Example: Bring to Front
Demonstrated on yellow square.
Send to Back (CTRL+SHIFT+[): Moves the selected markup behind any overlapping annotations.
Example: Send to Back
Demonstrated on yellow square.
Bring Forward (CTRL+]): Brings the selected markup up one level.
Example: Bring Forward
Demonstrated on yellow square. Two clicks are shown.
Send Backward (CTRL+[): Sends the selected markup down one level.
Example: Send Backward
Demonstrated on yellow square. Two click are shown.