Ok, maybe I should explain a little better...
A damaging ability does an amount of damage that is based on level and then it does extra damage based on the amount of AP/AD the person has. Example: Lux's ult could do 300 damage (This would be magic damage) and then it could do an additional 72 (that would be based on the fact that the Lux has 72 AP).
My question is, if Lux's opponent bought MR, would the MR offer this person resistance to the 300 damage, the 72 damage, or all 372 damage? From what I gathered, the MR would help against all 372.
What about an ability that scales off of AD? So, say an ability (one scaling from AD) does 100 damage and then an additional 52 (due to the amount of AD the champion has). The 52 damage would be physical, but would the 100 be as well? From what I gathered, I think the answer is yes. Then, kind of like I asked before, would an opponents armour reduce the 52, the 100, or all 152 damage?
And then, what if there was an ability that did 100 damage or something plus magic damage based on AP, plus physical damage based on AD, what would the 100 be? Physical damage, magic damage? Would it just depend on the champion?
Note: The AD example, I just made up the numbers. I play more AP champs than AD, and so I couldn't think of real numbers off the top of my head.