One of my tanks was empty, so I transferred all the fuel from the other tank into it by setting supply knob on the Caliber Smart Fuel System to the source tank (in this case, tank 1). Then I set the return knob to the destination tank (tank 2). Up until today, I wasn't using tank 1, so the fuel valve was closed. I opened the fuel valve on tank 1 since I set it to supply. I also opened the fuel inspection plate on tank 2 so I could hear and see the fuel entering the tank and to make sure I did not overfill.
I then set the small fuel pump in the Caliber smart fuel system to "manual" and fuel started transferring from tank 1 to tank 2. The fuel pump is rated for 50 GPH, so it takes a couple of hours for one tank to transfer to another. I believe you can transfer fuel while underway by using the engine fuel pump (?), and that it transfers quite quickly that way
I left the "Filter In" and "Filter Out" knobs set to the same filter as it is the one I have been using while motoring and I plan on changing the filter element shortly. Otherwise I guess you could set one filter for "in" and another filter for "out" and run the fuel through both filters.
After the transfer is complete, make sure and put the smart fuel system knobs in the desired position and close or open the appropriate fuel valves.
I drew myself a diagram so I could get my head around how this system works. I'm not sure it's 100% accurate, so I'll take a look at the hoses when I'm on the boat and verify.