The height of our mounts is always measured from the top of the Picatinny rail (or the receiver for direct mounts) to the center of the scope. In the case of a tilted mount themeasurement is made at the back plane of the rear ring.
So which height do you need? First off you need to know the outer diameter of your objective. Please note that "3-12x56" does not mean that the scope has an outer objective diameter of 56 mm - only that the objective lens is 56 mm in diameter. Different scopes have different outer diameters for the same lens diameters and it's not uncommon that different models from the same manufacturer feature different outer diameters even if the lens diameter is the same.