Colors can be assigned to applique steps. This setting instructs the program how to interact with the stitches in processes such as color sort or when removing hidden stitches. Applique positions will not have their stitches removed. Applique material steps indicate that there’s fabric that has been laid down, which will cover other things, not just where the stitching exists. Also, stopping the machine during applique is necessary, so if you color sort the file, the applique setting helps the color sort system add flags to keep the stops.