My C# application sits on the embedded box which has Intel motherboard and graphics chipset. ATI graphics card is put on to PCI express. Generally graphics card drives the v
Your question isn't entirely clear, so I'm not sure if the follwing idea will help or not.
Perhaps something very simple would suffice:
If the two graphics cards run different resolutions check the monitor resolution using:
System.Windows.Forms.SystemInformation.PrimaryMonitorSize
Similarly, if one card supports more than one monitor, check the number of monitors using SystemInformation.MonitorCount.