-- second-monitor-on.sh

#! /bin/sh
xrandr --newmode "1280x1024" 108.00 1280 1328 1440 1688 1024 1025 1028 1066
xrandr --addmode VGA "1280x1024"
xrandr --output VGA --mode "1280x1024" --rate 60 --right-of LVDS

# of course these mode lines will need to change etc.

-- xorg.conf
Section "Screen"
        Identifier "Screen0"
        Device     "Card0"
        Monitor    "Monitor0"
        DefaultDepth 24
        SubSection "Display"
                Viewport        0 0
                Virtual         2560 1024
                Depth           24
                Modes           "1280x800"
        EndSubSection
EndSection

# you will need to make the "Virtual" size a fair bit larger, 
# to fit in 1280x800 and 1920x1200 side by side you'll need
# Virtual 3200 1200