My personal favorite is bluegill, or sunfish. These really put of some vibration, and struggle when you put a hook in them. Others that we have had luck with is sucker chubs, bullheads, blue chubs, small carp, did catch one off of a frog once. Make sure you check the state laws for what is legal. I know in Minnesota it is illegal to use gamefish for bait(bluegills
I have read of people floating the river in the daytime using fresh cutbait, stopping at every log jam that has some depth to it. This where the flatheads hang out in the day time. I did get into one once while going for channels with dead chubs in the daylight, let it go towards the log jam, and once it got in front of it bam he nailed it. They don't spend much time in one spot though, 20 minutes, and if nothing move on. I personnaly like to fish at night on the sandbars when they chase baitfish into the shallows. Seen many of night minnows jumping for there lives from flatheads.
Another piece of advice is that when ever we are flatheadin, and we start picking up channels, it means the flatheads are not there. a 2 to 3 lbs channel is a nice meal for a 20 lbs flathead.