The gauge can be calibrated within -7% to +7%, but that may or may not be your problem. You can also set the fuel sensor type in the tank as well as tank capacity. You can download the manual for your gauge at one of the following links. It will give you instructions for setting the tank capacity, fuel sensor type and calibrating the gauge if needed. All of this should be checked for accuracy & you should start off with the calibration setting at 0%. After running the engines you can reset the calibration setting as needed.
Square Gauge - http://www.yamaha-motor.com/outboard/commandLink/CommandLink%20Operation%20Manual(Square).pdf
Round Gauge - http://www.yamaha-motor.com/outboard/commandLink/CommandLink%20Operation%20manual(Round).pdf
You can also use the gauge to look at individual engine information. With the ignition switch on press the "set" button to switch between information between each engine. Assuming you run both engines equally, both engines should show about the same fuel consumption. If one is a lot less than the other the fuel flow sensor on that engine is likely bad.
Testing each fuel flow sensor can be done without actually running the boat. Start by resetting the gauge to zero. Check one sensor at a time by disconnected the fuel line on the "out" side of the sensor. Connect a spare piece of fuel line and put the end in some kind of measuring container. Turn the ignition switch on and put the fuel flow display to that engine only. Next use the primer bulb to pump a measured amount of fuel through the sensor & then compare to what the gauge actually reads.