Personally, I would not have picked the Antec Nine Hundred v3 case with a GPU above the plain, non-Ti GTX 560. This is because the GTX 570 HD is already 9 inches long, and if a hard disk is installed in one of the upper (or center) drive bays, the PCI-e power connectors will end up being located way too close to the hard drive and hard drive connectors for comfort.
On the other hand, I would not recommend a RAID for the X79 platform unless you are willing to spend an extra $600 and up for a discrete hardware RAID controller card. This is because the Intel SATA controller now no longer has even firmware-assisted software RAID capability. Instead, RAID support on the native Intel ports is now entirely software-based using software that's also used with Intel's own workstation chipsets. And although the Marvell ports support RAID 0 or RAID 1, its performance will not be all that much faster in RAID 0 than a single disk does on the native Intel SATA controller in non-RAID mode.
Acutally my specs are already built. The VGA card is not that big and it fits perfectly on the case, and the drives also have plenty of space for the connectors. I managed to get a good cable management with everything going behind the motherboard tray and it's very nice and clean
I could consider the RAID controller card but that would be in the future because of budget restrictions (in a few months perhaps, when I could also maybe get more disks). So for the moment.. putting the two disks in RAID 0 (SATA II) will not give any performance improvement over putting the two disks separately?
A volume (whether that consists of a single disk or multiple disks in a raid configuration) is seen by Windows as a single volume and that single volume still is hampered by the half-duplex nature of the SATA connection. In your case, one SSD and one (raid0) or two volumes (single disks) will still have to adhere to the SATA half-duplex nature, but as single disks it allows reading from one volume and writing to the other volume at the same time. That is faster than waiting for the reading to finish (even though the reading is faster on a raided volume) and then starting writing on the same volume. I would suggest not using a raid with only two disks. Reading this answer, I realize this is not well explained, I find it hard to make an analogy, but consider it like a single street where traffic is allowed to flow in one direction only at a certain time. It does not really matter if that traffic can drive at 30 or 50 MPH on that single lane, because the lane is too short to notice that speed difference. Then the traffic direction is changed and the flow from the other side can start to move. That is the half duplex nature of SATA, but what happens when you have two lanes available for traffic (two volumes in Windows speak), each lane may be slower to move but the overall movement of cars is still faster than over a single lane.
Dear Harm, thanks a lot, that's very illustrative. This also disproves a previous though of mine, that in a RAID0 array, even if the two disks are considered as a single volume, you could have read/write at the same time.
Anyway, I guess then that I'll just use the two disks as separate. Would it be better to plug them into SATA II ports or into SATA III (Marvell) ports?
With single disks, you will not notice any difference in performance between SATA2 or SATA3 connections.