I was selected also on my recent AS flight from SNA to SEA. After I was searched, I just boarded with everyone else as I was sitting in Y. In SEA, they held up boarding so that the searchees get to board first. They even went as far as to go onboard and grab the people who didn't show up for the search. I was also told that if you are selected on your first segment, then you will be selected on all of your segments.