one line comes from the cruise control, the other line goes behind and under the blower motor and is plugged into a rubber grommet that goes into the car, near the ECM. Another line comes out of that grommet and it connects to the heater valve behind the turbo. Hopefully they havent been pulled out of the grommet because its a biotch to get them back in. Don't ask me why i know...
As long as the unit itself isnt damaged dont worry about it, just make sure the lines are connected, and stay connected, or youll have A/C and heater problems.