The way it is SUPPOSED to work as I understand, is this: Both tank valves should be on. The lever points to the tank you want it to draw from first. When that tank is exhausted, a red marker shows up in the glass window to tell you that you are now drawing from the opposite side. At this point you can move the lever to point to the tank in use. Doing that will clear the red marker. Then you can close the valve on the first (now empty) tank, disconnect and refill/replace it. When you do, the system will continue as is, and flip back over to the first tank, if it is now on, pressurized, and valve open.
In your situation, with only one tank open, the auto-shuttle could not work. It seems like it should have flipped with the handle when you switched sides. Might need some repair.