Try opening a terminal and running sudo nvidia-xconfig. I find especially with dual monitor setups I need to run this to get anything working properly when using the proprietary nvidia drivers.
nvidia-xconfig will automatically generate the configuration file for your monitor(s). If it doesn't generate it properly then try the following instead.
First a precaution run the following command to backup your current configuration:
sudo cp /etc/X11/xorg.conf /etc/X11/xorg.conf.backup
Run gksu nvidia-settings in a terminal. Choose the layout that you want for your monitors. When everything is done choose "Save to config file" and overwrite the original file. Reboot, this should have everything set up like how you choose. In case there is an error and you are unable to get a GUI back, enter recovery mode and the following two commands to get back to the previous settings
sudo rm /etc/X11/xorg.conf
sudo cp /etc/X11/xorg.conf.backup /etc/X11/xorg.conf