If you have a suction cup on the circle cutter, it will be easier to hold in place. But a three legged circle cutter is possible to keep in place too.
In both cases, one hand holds down the centre and the other operates the cutter. Make a test circle with no pressure to ensure before you start that the cutting bar will not bump into anything else on the bench. This also ensures that you have the circle to be cut placed appropriately on the glass.
To make the score start with the bar under your supporting arm and swing around to the other side of your arm until you hear the click or scratch indicating that you have come back to the start.