Please post case manufacturer and part number...
USB headers are normally either 5 pin (with one empty), or 2x5's with one hole blocked, to 'key' the connector so it can't be plugged in wrong.
The pins closest to the CPU are power - +5V
The next pin down is signal -
The next pin down is signal +
The next pin down is ground
on the right side of each header pair, the bottom pin has no connection...
Page 30 of your manual: