If you are targeting only large "trophy" size fish use big bait. I've used live suckers 8" long in the past with success. Sunfish, bluegills, small mouth bass, bullhead, and shad all will work To a giant flathead if it swims it's food. as to depth it depends on water depth, water temp, river or lake, and too many other factors to mention I set one rod on the bottom Carolina rig and another under a float.

Good Luck
Matt