The ball in the inclonometer shouldn't be centered when you have an assymmetrical thrust situation. You should try to fly the airplane with minimal side slip. With assymmetrical thrust, wings level and ball centered, the airplane will be slipping due to the operating engine pulling the airplane slightly sideways. Therefore you should compensate by putting the ball slightly (approx. 1/2 the ball width) into the operating engine (more rudder pressure). And also as widely known, bank 3-5 degrees into the operating engine to use the horizontal component of lift to counteract the rotational effect resulting from the assymmetrical thrust."wings level, ball centered"
If you've ever done drag demos, you'll appreciate a noticable difference in performance when flying the airplane "wings level, ball centered" versus "sideslip eliminated, bank slightly into operating engine". Vmc changes also, because you're utilizing more sources of counter-forces to maintain directional control - not just the rudder.
The ultimate proof and expedient method of understanding this, is by attaching the yaw string to the windshield and try for yourself.