SLI board question

If I were to purchase an SLI board but only use a single x16 card does it matter which slot I use? I noticed a lot of them have the top x16 slot right above the x1 slot (such as the DFI lan party boards) I have a x1 card and my video card would take up this slot if I was forced to put it in the top x16 slot.
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More about board question
  1. Have a look at Abit KN8 SLI as it has 2 PCI-E x1 above the top x16 (or indeed the better AN8 32X has 1)
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