Alright, your question is pretty confusing.
Let's summarize. You have a motherboard that uses PCI-e x16 and you want to know what's the deal with PCI-e gen 2.0 and if you can run it.
The anwser is yes. PCI-e is backwards compatible. That meas that you can run PCI-e 1.0, 2.0 or even 3.0 in the same slot as they are physical the same.
Let me explain you this way. PCI-e x16 is the speed as PCI-e x8 2.0. And that speed you wont bottleneck most cards out there. You will need a GTX 780, Titan or AMD HD 7970 highly overclocked to fully utilize the bandwidth of PCI Express.
The biggest of your problems are not compatibility. It's your processor, IT WILL bottleck many mid-high end card.
Choice a single nice card, lets get HD 7950 that are pretty cheap and well performer, wait some time a upgrade the whole system, at least CPU, mobo and RAM.
Let me say you, that think most people say "get AMD GPU to run an AMD Processor they will work better, or When you build an intel build get an nVidia card, they work better" Thats a myth, a feeling that people has about paring processor and gpu of the same company will give better results than mixing. That's pure ignorance. It's completely false. Even, not long ago Tom's Hardware did a review showing that Intel works a little better with AMD GPU's than with nVidia GPUs. That's very subjetive and it change every year... So dont look at paring same company products to have a better system. Get what's better for your money!
Thank you.... I am currently looking into buying a GTX 760 for my OLD ASUS Crosshair AM2.