Yes, that really would be a desirable option! At the moment you can only save this setting permanently by switching to XOrg and using the terminal program xrandr (or arandr, that is the gui for it) with a script that is launched at start.
With the flag --above you can set the position. First find out the I.d.s of your monitors by running xrandr in terminal. When your laptop monitor maybe is eDP1 and your second monitor HDMI-1 a possible script may look so:
#!/bin/bash
xrandr --output HDMI-1 --above eDP-1
or if the second monitor is connected via Displayport
#!/bin/bash
xrandr --output DP-1 --above eDP-1
You could also add refresh-rate and resolution of the two monitors.
Take a look at this thread: