When you enable dual monitor in BIOS, the onboard video controller is enabled as the primary video device, so it will be used to display POST messages. You can extend display to your add-in graphics card after OS loads.
However if you're running Windows Server 2008 or Vista you may have a problem. Basically it's because that Windows 2008/Vista requires same WDDM driver for dual display to work. No such limitation for XPDM driver (2003/XP). See http://www.intel.com/support/motherboards/server/sb/CS-030728.htm for details.
Yep, Edward, this is invariably the problem. It is also why my homogeneous-Multimonitor support worked until I pulled one of the PCIe graphics boards out. hey were working on the identical WDDM stack. Now my onboard GA and my NVidia are on different drivers and the problem is as described in the Microsoft Technet flash: http://technet.microsoft.com/en-us/library/cc756392%28WS.10%29.aspx
Oh well. Here's what I did instead: my single PCIe NVidia card still supports multiple monitors, just through DVI and DisplayPort. So I have disabled onboard GA and am running both monitors through the single PCIe card and two differing cables.