Look at the diagram of your motherboard on page 1-6 of your manual (download HERE
). At the bottom of the board past the last pci slot, there are several connectors (headers) to supply usb 2 output to your case front or other area (item 16 in the blue circle). There is also a usb 3 header on the front of the board next to the 24 pin power connector (blue circle 7). Those headers (both usb2 and 3) are meant to be used for your front case connections, or for permanent usb devices, like a card reader, that have a usb pigtail. See pages 1-26 and 1-27 of your manual.
On the rear of your board where the stack of connectors are are several usb ports intended for keyboards, mice, etc that use the familiar usb plugs. See page 2-13 of your manual. There are 2 usb 3 ports and 6 usb 2 ports.
Let me know if you have any other questions.