I think your forgetting that the two different loads will have entirely different POI. It won't just include up/down changes but may also include some side to side movement.
First you need to zero your scope for your primary load. Reset your turrets to zero. Then shoot a group of your secondary load. For example, zero your first load at 100 yards and zero it. Then shoot your secondary load, let's say it impacts .4mil up and .3mil right. We would then need to dial the scope down .4mil and left .3mil for point of aim to equal point of impact on the second load.
We can then run our ballistic calculations for both loads. On the first load, everything on the table is right on. On the second load, you need to subtract .4mil from every elevation adjustment and dial an extra .3mil left for every windage adjustment.