Yes, the subsonic ammo is going about 1/3 the speed of the supersonic round. Therefore it drops a lot more. The point of impact shift is a repeatable shift, so learn how to correct for it, and you will be on target. I would also learn the trajectory of the subsonic rounds.
I also make/sell an SBR load that runs 1040 fps in the 11" barrels. When you run normal subsonic ammo designed for a 16" barrel, the SBR's lose about 100-150 fps on an already slow round. This SBR load gets your speeds up for more energy on target. http://dallasreloads.com/product/sbr-208-grain-a-max/
If it were me i would zero my turrets with supersonic ammo and then take a white piece of tape or nail polish and line it up with 10moa and 4moa on your windage.think of it as 2 selector swithes your turning them to supersonic or subsonic.that way you will have two 100 yard zeroes.if your zero changes take tape off or remove nail polish and repeat.
^^ Good idea