Not quite. If skulls are segregated by morphology AND time and/or distance that is evidence that there are two distinct species, i.e. if the big skulls are always over here and the little ones are always over there (or the big ones are always in this layer and the little ones always in that).

But if you find different morphologies together in the same time and place that is evidence that they were all members of the same species because it is rare to have two different species occupying the same ecological niche.