I was going to wait and see what others said but I guess I'll take a crack at it. Before you do anything be sure to backup your xorg.conf. Run all commands I specify as root user.
cp /etc/X11/xorg.conf /etc/X11/xorg.conf.bak
Do you know what graphics chipset you have? (nVidia/ATI/whatever) Sometimes the vendors provide utilities which greatly simplify the process of modifying the xorg.conf to take advantage of unique features of the vendors binary blob drivers.
I'll continue searching around but I haven't found any open source implementations of nVidia's TwinView. I'll post back as I find more material.
never mind about the graphics chipset question. I figured it out from reading your xorg.conf
edit 2: xrandr
looks like it will be able to possibly accomplish what you wish. I found an example of it in the gentoo wiki
. I'll see if I can formulate a command which would modify display modes of individual monitors.
I have found two links which are useful: one is from ubuntu
and one is form nVidia