[ubuntu] Problem Installing Ubuntu 16.04 with dual-graphics system (i7-4790K/GTX 960)

I recently attempted to install Ubuntu 16.04 on my system, but I have run into a problem that I have never faced before.

The computer is set up with two monitors: a 55" TV being driven via HDMI by a GTX 960, and a smaller 23" Samsung monitor being fed by the Intel graphics over DVI. I had to set the system up this way in order to be able to use QuickSync with several Windows video encoders.

Using both a USB stick and a live DVD, I was able to boot into the login screen, but the problems began right there. The Intel monitor had no image, and the 960-driven TV flashed on and off constantly, and was slow to respond to any inputs. I eventually had to physically uninstall the 960 and install Ubuntu with Intel graphics.

What steps do I need to take in order to install 16.04 so that the flashing problem is solved and I can have both displays working, or at the very least the primary one (the 960) working? I need to keep the 960 in the system so that I can use it with Blender.

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