i recently discovered arandr, a GUI for xrandr. if you are using nvidia twinview and experience some problems with an always changing screen layout on every boot, try to use ArandR to create a script that reconfigures your screens using xrandr.
simply configure your screen layout the way you want it, start ArandR and hit Layout→Save As and save it as a shell script.
on my system (running xubuntu) i had to add a
before the randr line in order to wait for the screens to be initialized and then run the randr instructions. i put the script in autostart and voilà, my screens now always appear as they should.