Use the leather gloves for this step! Glass conducts heat incredibly well!
Be sure there is no water in your iron and set it to the highest setting. Once your iron is incredibly hot begin applying it to the back of the paper. Try to cover all areas of the stencil with equal pressure and heat. This step is tricky. Not enough and the toner wont transfer. Too much and the paper may bind to the glass. Glossy paper transfers the easiest, but also has a higher tendency to stick to the glass. Keep in mind that quick changes in temperature will cause glass to crack. Let these slowly cool at room temperature. Resist the urge to run them under the sink!