You are right, for this board you will need to have the connector 2X4 12V for the CPU on the Power Supply, it does not work with the 2X2 12V.
Now regarding the drivers for Windows 2008, last time, i suppose that you know Intel Desktop Boards dont support Server OS.
But the good news is that, even that it is not supported, I tried Windows 2008 Enterprise 32 & 64 bits on the Intel DQ45CB, and i installed the latest drivers for Windows Vista, everything worked fine, except for Network Drivers which you will need to install it maually.
Website for latest Drivers: http://downloadcenter.intel.com/Product_Filter.aspx?ProductID=3018
Install the drivers in the following order:
Ir Driver if enable in the bios
Please it is good to have the latest bios version as well
Hope this helps a bit.