When both riders are getting off the bike, at an ice cream store or at the end of the day, for instance. The captain should stop like he would at a light. The stoker should then get off the bike and get clear. The captain should then get off the bike, making sure he is aware of the handlebars in the back. I try to avoid making standing sound difficult.
Fear seems to be the biggest problem.
If you don't believe that it is difficult, standing can come quite naturally. The captain should announce his intent to stand. The stoker should acknowledge. This is important because the stoker may be doing something else and not have his or her hands on the bars. It is even more critical if you are standing on flats.