Basically you have +5v, ground, Data+, and Data- wires; thats 4 wires per USB port.
If you have a single two row plug then look at the connector end where the pins go in. One of the holes will be filled so that you cannot install it incorrectly (without some effort - LOL). Match the filled hole with the missing pin for the USB5/6 connector on your motherbd.
If you have individual front USB wires they should be labelled enough for you to figure out which is which. Something like 5v-1, 5v-2 D+1 D+2...
THis means that you 5v for USB port 1 and 2; data+ for USB port 1 and 2. (etc..) Keep all the port 1 wires together and all the port 2 wires together.
Use your manual to identify which is which pin on your motherbd. (note that one will not have a wire connected (NC) to it; its just so you can't put in the (somewhat standard) 5/4 pin connector on it.
From page 1-25 of your manual and using the USB56 connector
Connect your usb port 1 wires to the top row
top row is USB 5 and from the back to front of the case:
5v D+ D- GND NC
5v D+ D- GND
The bottom row (USB6) does not have the last (NC) pin but uses the exact same wiring order as the 4 above it as you see. Connect your USB2 wires here.
If you have more front USB port wiring you can repeat the process with the USB78 connector on the motherbd.