Since the hard disk drive LED and your case LED connector aren't matching up (I assume), you could take the connector apart and rewire it so it does.
As to the USB ports, you can attach the ones from your case as shown in the attatched file. Because of yet another discrepancy between mobo manufacturers and case manufacturers, these probably have different labels, too. USB+5V is the same as VCC. It doesn't matter which side you connect those to. "USB_P5-" and "USBP6-" is the same as "Data0-" and "Data1-". Same thing goes for positive. Connect two grounds (doesn't matter which) and leave "NC" open.