In the Device section of xorg.conf you need to put:
Option "MetaModes" "<resolutions>"
I have a widescreen monitor and a standard resolution monitor, so my metamodes line looks like this:
Option "MetaModes" "1680x1050,1280x1024; 1680x1050,NULL"
The resolution of each monitor needs to be separated with a comma, and different metamodes need to be seperated with a semicolon. The NULL option in the second metamode switches off my second monitor, which I use when playing games that I don't want to span both monitors.