In general, USB2 stuff works no issues on USB3 ports. Of course since I said "in general" you can guess there are some "in specific" cases where it doesn't :). If you have Windows 8 and an Intel chipset that is a 7 or 8 (or newer) series then USB3 should Just Work(tm). It'll be on your Southbridge chipset, just like USB2, and you shouldn't have to care about what port is what. If not, there are two potential issues I know of:
1) Windows 7 doesn't come with USB3 support. This means you have to install a driver to make it work. This also means that upon install if your mouse and keyboard are on 3 ports, they won't work.
2) There are two kinds of USB 3: NEC and Intel. Older boards, 6 series or earlier, didn't have integrated USB 3 so there was an NEC chip (also called Renesas) that added it. This had additional issues. You couldn't install from those ports, and sometimes BIOSes didn't support them properly. Also for video interfaces, they could have speed issues. This can be true even in Windows 8.
Now on your listed system, the USB3 ports are Intel ones, they are integrated in to the southbridge. So no issues there. Since Intel provides proper 7 drivers, you aren't likely to see any issues at all. Of course as Scott noted, if there's a problem try a 2 port, but your only issue is likely to be that you need to install drivers before Windows can use them. Should you choose to upgrade to 8/8.1 then that'll no longer be needed.
USB is actually fully backward compatible, when you plug in an older device it just steps down to the older standard (and in the case of 3->2 actually uses different pins). The main reason there were issues with 3 in the early days was the NEC chips, since they were actually separate, not integrated. With new hardware, that is gone, and with Win 8 and up, there aren't going to be any software issues either, 3 ports will just be like 2 ports, but faster if something happens to use it.
post edited by Sycraft - 2013/10/06 04:20:10