PCIe - do slots matter?

So, perhaps a silly question, but like I've said before, my last dedicated GPU was a 3Gfx Voodoo II

My little beast of a motherboard comes with two PCIe slots that can run as 1*x16 or 2*x8. So far everything is perfectly fine and understandable. However, what I wonder about is wether it matters in which slot is the GPU installed? There are no labels next to the slots and there are no information in the manual. Would I be correct by assuming that both bottom and top slots will run at x16 when only one card is present?
Thanks!

Both of the motherboards I've owned with 790X chip sets the top one is 16X and the bottom one is 8x (regardless if the top one is filled or not). I still use the bottom one because of the heat and because the difference between 16x and 8x is virtually nil.

Sometimes you can tell by the number of pins in the PCIe socket. If one of them ceases having pins halfway through, that's the 8x one.

With anything but a grade A top end GPU, it really doesn't matter whether it's 8x or 16x.
Even on a top notch gpu it's only a few percent. (1-2% on 5870, tested. Possibly 2-4% on a gtx580? Guessing there)

Psykoikonov said:

Both of the motherboards I've owned with 790X chip sets the top one is 16X and the bottom one is 8x (regardless if the top one is filled or not). I still use the bottom one because of the heat and because the difference between 16x and 8x is virtually nil.

Click to expand...

Bobnova said:

Sometimes you can tell by the number of pins in the PCIe socket. If one of them ceases having pins halfway through, that's the 8x one.

With anything but a grade A top end GPU, it really doesn't matter whether it's 8x or 16x.
Even on a top notch gpu it's only a few percent. (1-2% on 5870, tested. Possibly 2-4% on a gtx580? Guessing there)

Click to expand...

Great, thanks for the info!
Yes, that's the only reason I'm asking... when I get a GPU I'd like to run it on the bottom slot. Tad bit better for temps and I still get access to PCIe 1x, although I doubt I'll need it because the onboard sound supports lossless audio anyway.
Will give a looksie and see what's with the pins, although I guess it's safe to assume that those slots are designed the same way as others are.
Thanks!