One line is larger than the other at the rear heater hose ports. I used a section of the stock hose to adapt it to 5/8" heater hose. Simple run the two lines to the heater core. It does not matter very much if you mix them up, it will still work.
If you are talking about the vent hose on top of the thermostat housing it must be used and it must be connected to an expansion tank. The expansion tank should have a small port on the top (not the port under the pressure cap). The purpose of this small hose is to vent out any air that may be trapped in the system. Air will occur naturally so it should not be simply connected to a bleeder tap but connected permanently to the pressure tank.