My youngest son is probably the best I know on flatheads. He goes out and specifically fishes for them below our dam. Not only is he an accomplished noodler,(reaching into underwater holes and dragging out monster flatheads), he's very knowledgeable about bait fishing for them also.
He likes to take small live bream and hook them just under the back fin and throw them out with just enough weight to hold them on the bottom. The trick, he says, is not to set the hook when you first see the strike. He says that the flathead will strike his prey a few times killing it and then he will move off a short distance with it and swallow it. At this point you pick up your rod, reel up your slack, and set the hook.