Now I am going to show my ignorance. It has been a while since I messed with the Nvidia proprietary drivers. But, I expect the "nvidia-settings utility" to be in the sub menu under applications. I would suggest start the system up with but the one operating monitor connected, when the sytem is booted connect the 2nd monitor and see if "nvidia-settings utility" finds the 2nd monitor.
Too see what is in the control file "/etc/X11/xorg.conf" fire up a text editor - the file is a text file.
Post the file's contents back here and maybe I can flounder my way through it, to our mutual comprehension. Hopefully others will chime in with their advise;
gksudo gedit /etc/X11/xorg.conf
for "/etc/X11/xorg.conf.d" as it is a directory, let's see if there is anything in it to even look at .
I really do anticipate this is but a
ls -la /etc/X11/xorg.conf.d