The way mine is set up, the Beetle Bits does not start at "0", but that doesn't really matter. I have my ruler marked where the cutting line is - it is aligned with the yellow arrow on the Flying Beetle Cutter. I place my glass right at that line. (This is a different color of glass because the original picture did not turn out right.)
For this tutorial, I'm making 5/8" squares, so I count over 5/8, and then move the glass over to that notch on the ruler. I lightly press down on the Flying Beetle cutter and push upward until the whole sheet of glass is scored. If you like sliding the Flying Beetle cutter down the bar, start at the top of the glass, press down on the cutter, and slide the bar down.
I plan on cutting a full sheet, so I continue down the ruler sliding the glass, scoring with the Flying Beetle cutter until I run out of glass. The first arrow on the left is where the actual score line will be. The second arrow is a scored line. The other four arrows indicate where I will be sliding the glass next and scoring.
I then flip the glass over, turn it 90 degrees, and score that side of the glass as described above. I flip the glass because it is not good for your cutter to crisscross over a previous score. The cutter won't last very long if you do. (For thick glass or mirror glass it is unavoidable, and all scores have to be made on the same side of the glass.)
When running the scores, run (break) the glass in half, down the middle. Then you take each half and run (break) the glass in half again. You keep halving the glass until you are down to two pieces. By halving the glass each time you break, you are keeping even pressure on either side of your running pliers, which will give you cleaner breaks.
I turn the glass over and continue running the scores on that side of the glass. Again, I break the glass in half, half again, half again, and so on until I'm down to two pieces. Good clean cuts! Nice even squares! The squares will be as accurate as you were measuring against the ruler.