Okay, so some basic terms. The monitor section defines your physical displays, including horizontal and vertical refresh rates.
The modelines below are to define combinations of refresh rates and resolutions, in case the monitor does not advertise that to your box.
Then comes the device section, which defines your graphics cards and the drivers used for them.
The Screen section defines X screens where content will be displayed. The Serverlayout section defines how the Screens are displayed if there are multiple ones.
Terms in xorg-speak could be confusing a little¹, but you get used to it. Maybe check
http://en.wikipedia.org/wiki/X_Window_S ... menclature and also the headings in
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man xorg.conf
which explain the sections.
There are also Viewports and Virtuals, but best forget about them.
For something more practical, as you want to use to monitors, my suggestion would be as follows: Move away/rename xorg.conf and see if something changes so that you can change resolution and layout on the fly.
The modelines you have for your primary monitor may be conflicting with xrandr usage of cinnamon. Hence as root
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mv /etc/X11/xorg.conf /etc/X11/xorg.conf.orig
Then Ctrl+Alt+Backspace when all other applications are closed to restart X. If the X server doesn't come back, then Ctrl+Alt+F2 and login as root and move it back.
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mv /etc/X11/xorg.conf.orig /etc/X11/xorg.conf
