Unlike some of their other relatives, Flatheads are primarily predators. Although you can catch them on cut bait, stink bait, etc that you would use for channel cats, LIVE large baits will out produce 100 times over. Try to catch some bullhead or bluegill from the river when you get there, or if you can find large suckers at a nearby baitshop, those work great too.
Flatheads also spend something ridiculous like 80-90% of their time in wood structure and log jams. So concentrate your efforts around wood. Deeper holes are a 2nd best, but log jams are king.