Does an onboard video affect the X windows configuration?

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http://askubuntu.com – Does the onboard video on the motherboard affect the X windows configuration? My system has onboard and pcie video. The onboard video is a NVIDIA GeForce 7025 GPU, On Board Graphic Max. Memory Share Up to 512MB(Under OS By Turbo Cache). I have a pcie dual head video card installed with two monitors. The video card is a GeForce 8400 GS, with 512mb memory. When installing Ubuntu 12.04, only one monitor worked. When pulling up system settings- Displays it shows a laptop. This is a desktop pc. I did get both monitors to work using nvidia using twinview -- A complicated process! When che (HowTos)