Actually it has 4. USB 3.0 Header is next to the ATX connector and SATA 1 and 2. That will go to your 3.0 ports.
You can then use one of the 3 others for the two remaining 2.0 ports. (If there is a separate connector anyway)
Generally one will be coming from the chipset PCH, the other two were added by the board manufacturer.
Quite a few things can be plugged into those. More USB ports of course, Digital fan controllers, All-in-one cooling systems use them, RGB LED arrays, and all kinds of goodies.