I only make cheese from raw milk, from my own cow. I know my own practices, I know how clean she is and I know how healthy she is. Therefore, I don't feel a need to pasturize my milk before drinking it or using it to make cheese.
If you do make cheese with it and it is aged for more than 60 days, you won't need to pasturize, either, because the developing acidity in the cheese will be enough to kill off any microorganisms anyway. I would not mix the milk, as the store milk usually requires the addition of calcium chloride for cheesemaking, while raw milk does not.
As to the skimming question, it depends on the type of cheese you are making. When I make cheddar types, I leave all the cream on. When I make mozzerella or parmesan, I skim the cream.
I will let someone else address the "difference" question, as I've never used pasturized milk for cheesemaking.
Have fun with it! $3 a gallon is downright cheap for raw milk, IMHO.