When you have cut a piece from the main sheet, it is easy to turn it over and work on the clear rather than the flashed side. It is essential to know which the flashed side is if you are going to do any etching of any kind. So, as soon as you have cut the piece, mark the flashed side. This will keep you certain that you are working on the flashed side.
Another method to keep track of the flashed side is to mark across the intended score line. After scoring and breaking you will have both pieces of glass marked. All you need to do is make sure you always mark the same side - flashed or clear. Some like to cut on the clear side and some the flashed side. All you have to do is to determine which your practice is.