Renee, there is a walkthrough here at GameBoomers (I don't know if it is the same one that is on the CD or not)--here is what it says: "Once in the Control room, turn to your right and click just to the left of the thick metal pipe. Notice an empty place, place the thin metal pipe in that space. Now the left water tank is almost empty, make it so that the right one is almost empty. Leave and go back to transporter and go to Zn."
So it sounds to me as though both tanks should be almost empty...
