I wanted to automatically configure second monitor plugged into my laptop as above internal LCD, and I was prepared to allocate few days for this task. But, in recent X.org servers this has gotten much better, so it's enough just to add following to .xinitrc:
xrandr --output DVI-0 --auto --above LVDS
xrandr --output VGA-0 --above LVDS
There is also
grandr (with package in Debian) if you want point-and-click functionality.
Don't work on single monitor, having dual monitor again is such productivity boost :-)