well, I'll explain more for giving you a bit of cheek.
The AFM is part of the ECU system and doesn't care what is sucking air though it, as long as whatever is sucking air thought it (turbo, vacuum cleaner, squirrel) isn't maxing it out.
The Turbo charger has absolutely no effect on the AFM when it comes to changing, just don't max the afm out. Since S1 and S2 turbos flow the same, you won't notice the difference at all.
Everything will be ok.
Not intending this as a crack - But Rich Flavour, you might want ot read up on how these systems work to get a better understanding.