When you activate Surround you'll get to a screen that lets you rearrange the displays so that it looks correctly on the desktop. All you have to do is select "identify displays" and numbers will appear on the screens then you rearrange the monitor icons in the box to match what the numbers your monitors displayed. So fir instance if your displays are listed as 2 3 1 when you click "identify displays" you must rearrange your monitors in the box to also match this.
 
But if all you want to know is if it matters at a basic level how you have your monitors hooked up, then no it doesn't. As long as you have them hooked up correctly to the video cards it doesn't matter what the arrangement is since as I posted above you can rearrange them in the settings. But personally I like to hook the center monitor to DVI 1 so that my bios, post and Windows loading information appears on the center screen. DVI 1 is on the top card on the DVI port that is closest to the motherboard if you were wondering.