Start with a template as your base layer. Then add a second layer and use your fill tool to make it completely white. Then make it transparent. Then create a third layer and paint in black the parts you want to be transparent using your template as a guide. Then when you are ready to save, make the second white layer opaque again and save. This will hide all of your template underneath. Now when you use your transparandy map, all the black parts will be transparent and all the white parts will show.