Mil-Dot Ballistics uses ballistic profiles that represent a combination of a specific, rifle, scope and load. You can set up profiles that represent different loads in the same rifle.
First lets start off with your primary load. Go to the range and zero your rifle for that load at whatever range you want. Create a ballistic profile for this rifle, scope and load combination.
Next, without changing your scope settings shoot your additional load at the same distance. Note how high or low the point of impact is in reference to your point of aim in inches or centimeters. Now clone your primary ballistic profile, modify the load data as necessary (bullet info and muzzle velocity), and input the elevation difference of your point of impact in the "Y Intercept" setting. Negative values indicate that the impact was lower than the point of aim; positive values indicate that the point of impact was higher than the point of aim.
Assuming that the bullet info and muzzle velocity are accurate, you now have two ballistic profiles that will accurately represent two different loads in the same rifle. This process can be repeated with as many loads as necessary.