I guess my question is what CPU cooler are you using that can reach all the way to the first PCIe slot? Thing must be huge! You usually HAVE to use one slot if you are using only one GPU. You can try it in the 8x slot, but be prepared for it to not work.
They are both 16x PHYSICAL slots, but the bottom one has only 8 lanes connected. This is good. You can plug any PCIe device into a 16x slot and have it work. If its a 1x card it will work. If its a 4x card it will work. It will use however many lanes are available, up to the limit its designed to use. Why we put 1x or 4x slots on motherboards I'll never understand.