Lets say you make a layer with only freckles. And then let that layer be on top of all other layers, and then use the Transparancy tool? Or maybe if you place the layer with freckles under the top layer? And use the transprancey tool again?
And maybe even make 2 or 3 layers with freckles or other dot´s in different shade´s of dark. Giving some feeling of individuality to the freckles and dot´s ?
Maybe worth a try.