On a FI engine they don't help with atomization seeing as the goal is to have the injector spray directly on the back on a closed intake valve just before it opens, the heat in the valve does wonders. You are supposed to leave the surface rough, but you'll find that surface texture doesn't make a big difference at all on a flow bench (some people will argue that it doesn't make a difference at all).
I would suggest not porting it at all, odds are it will work WORSE than it did before, especially if you dont do anything to the upper. I've had cars make 360rwhp NA through a untouched cobra intake.