Novice question about SLI...is there a primary slot?

I bought a rather large video card recently, the Sapphire HD 2900. I'm looking to upgrade the rest of my equipment. The card is so gigantic that on my current board, the back end of it including the fan, is rest on top of half of the motherboard fan. My motherboard temps haven't risen hardly but I still don't like it. Going through newegg looking for a new motherboard, I've noticed a lot that have the northbridge or southbridge heatsink/fan in a spot where my card would probably interfere. So I started looking at SLI. There are a ton of boards that would accommodate my card if I could put it in the PCI x16 slot farther away from the CPU on a SLI board. I just wanted to make sure that I wasn't required to put it in a specific one if I was only going to be running one card.

 

Just to clarify, my basic question is this. Does it matter which PCI-E slot I put my graphics card in on a SLI board when I am only using one graphics card?

 

im not shure if it matters which one you out it in. but on all the sli boards ive had it says on the board itself wich slot to put it in. if it doesnt. ide put it in the top one. if it matters and you put it in the wrong one. it wont hurt anything. so go ahead and try the top slot. if that doesnt work, try the other one.