The guy I got to fit my front screen fitted the seal to the windscreen then fitted it as far as I can remember, my rear was already in but i would guess it fits the same way and the seal pulled in from the inside, I left the front out to put the headlining in.
Front seal only runs up the sides and over the top, rear surrounds the screen completely.
3dr had an inside finishing trim also but according to ford when I contacted them the sapph didn't but not 100% sure that's right although it didn't do anything and can hardly see it.