The best way to cut a pattern into stained glass is to use a traditional technique and place transparent glass over the pattern. Ensure that the lines of the pattern follow the proper allowances and cut the glass along the inside of lines of the pattern.
If the glass is not transparent enough to clearly see the pattern, use a light box or table under the pattern and glass. If the glass is dense and opalescent, trace the pattern onto the glass by placing a piece of carbon paper face down over the section to be cut and marking out the section. Be sure that the proper allowances are made before cutting along the lines of the pattern.
Another options is to tape a paper template to the glass with double-sided tape and cut around the paper. The paper can be traced onto the glass with a felt tip pen if the tape does not secure the paper properly. Mark any important information on the paper pattern, such as the direction of the grain in the glass or particular colors for the pattern. Cut the largest pieces first and then work down to the smallest pieces. Make sure the cut pieces are stored away from the work table so they are not mistaken for scrap or pattern pieces.