Keep your stoker happy. Do what makes both riders feel comfortable. Trading positions is good, since it allows each person to understand the workings of the other position. If you are close in size, you should be able to change positions. This may take some effort on the part of the captain.
Good stokers are special people.
We trust our captains completely and don't steer the bike from behind. This takes a little effort and practice. It also takes complete trust in your captain. Some people are unwilling to give up total control of the bike, and when they are stokers, they make a ride miserable. If you plan to trade a lot, adjustable stems are probably a good idea.