I wouldnt flat it, do another coat of black and get a decent finish. Sounds to me like you might be too far away and the paint is drying before it hits the car giving you a dull overspray effect in places. With base coats i find its best to do a couple of light coats then one heavy one as much as you can get away with without running.

Im no expert but have done a couple of full resprays and learned the hard way.

Also dont expect your basecoat to look like the rest of your car, it will look completely different when the lacquer goes on, saying that you still dont want the bit you have sprayed to look patchy.