Make sure the odometer matches actual.
Then you have to adjust the amoount of gallons you put in.
Ideally, the manual states to fill it up for the first fillup (the manual says to the first click, but if you're vented like mine, until you can see the fuel - no adjustments to be made.
For the 2nd and subsequent fillups, fill it up, then adjust the amount of fuel put in - the SGII indicated more then I had, so lowering the gallons raised the MPG - to pretty close to my hand calculated value. For the 2nd, it also recomends going to the same pump as your initial fillup.
Some members recomend going 50% of your correction - I was departing Raleigh to move to KC, so I went 100% for all corrections. The AVG value for a highway run is very close to my hand calculated MPG.
It doesn't seem to matter if your car has some performance enhancements made either - I have both bigger injector nozzles and RC2 on my Beetle.