The way it usually works is this...the use of a courtesy runner is based on your batting lineup...If you are batting 9 (or 10 with the EH), and have others on the bench, any bench player can be your courtesy runner. If your team is roster batting, then the player who made the last batted out is the courtesy runner. If the kid who made the last batted out is already on base, it reverts to the last batted out before his.
Jon