The position doesn't really matter- - -just be sure the springs aren't carrying the weight of the vehicle. With the way torque tube rear axles are pivoted at the spring mount, there can be a considerable amount of downforce exerted on the tube under some conditions. Since it's already disconnected the danger is probably minimal, but if you're going to be moving the tube up and down, it's better to err on the side of caution! Pivoting the axle tubes on the jack stands can also add an unwanted hazard.
Jerry