In general, if you set your window headers at the same height as your door header, you should be able to match them up pretty close. If you want, as an examle, exactly 3-3/8" from a particular lap joint on your siding to the top of all of your door and widow trim, you will need to have your windows on site, see where the trim will lay, and set your windows to that. As for the brick mold, that is totally up to you. If you want everything the same, you can add it to youir windows, or you can remove it from your door casing. As long as you are matching everything else, just look at how they did it on the house, and follow that.