I use mine in manual mode (without the rod) for rifle and only use three of the four holes in the turret. When I load pistol, I use all four holes and the indexing rod.
One thing that confused me, however, (well, one of MANY, but we'll just talk about this one for now) is that the red plastic round cases used to hold turrets with dies installed only really work well with three dies, not four, and even then they stand too tall in the case. It's fine when they're sitting on the shelf anyway, but you'd think they'd make some of the correct size and number of holes. I solved this with a custom base made in my woodshop, but...