if you are on nvidia, just set them up from nvidia-settings, you can move them around and then save the configuration
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You could possibly do this with xrandr where source1 and source2 are the names of your two monitors.
xrandr --output source1 --left-of source2
If your desktop environment has a monitor settings option, that might be more reliable.
X12?
About your problem: You can configure your monitors through the nvidia-utils and then generate a xorg.conf file for these settings.
typo. i meant x11. anyway when I get home i'll try using nvidia-utils
I thought you were using some obscure X11 fork, lol
you got also give arandr a try, as it is a GUI to xrandr and you can move your virtual monitors around a bit, until it matches the physical locations/orientations