This might sound a bit silly but most Video Card have many video output ports in the back, others have two DVI. For example, on my HD5870 Does it matter if I connect the DVI cable to the 1st or 2nd DVI port of the video card (this is when using single monitor only). Does it have an impact of the FPS of games?
From a performance point of view, no difference.
If you have two monitors attached, one of them will become the boot or bios display monitor.
If you care which is which, connect , or exchange them accordingly.