The Monitor Preferences does not have an option to set which monitor is the primary. I can set it with xrandr, like this:

xrandr --output DVI-I_2/digital --primary

But this does not work for a "normal" user. It would be very useful to have this option, because some gnome apps opens by default on the primary monitor, like the panel for example. If the user have plugged the monitors on the graphics card on the "wrong" order, the panel would open on the "wrong" monitor. It can be dragged, but it would be annoying to have to drag each app.