My question is, do I just link the two sets of wires and plug in then the plugs to their perspective housing?
Yes you can do that. I spent the $10 for the vehicle specific harness so I didn't have to splice/solder wires.
With the bag that included that harness in your glovebox, there probably are a couple relays that need to be added to your distribution box. One is to make the trailer brakes work, connect from the brake controller output to the 7-pin harness at the back of the truck. The other relay is to charge the trailer battery while connected.