"Does the species of fish you are using make a big difference in terms of production?"
......YES
I prefer to use baits that are natural to the waters i fish, meaning what the flatheads are already eatting every meal. Plus i dont buy baits...to many baits to be caught myself with the right equipment.
Suckers of all varietys, chubs, gills, rockbass, LM bass, sheephead,bullheads ect.
Spring i use smaller baits live 4-6" long, also fresh cut baits.
Summer sometimes they want live, sometime cut bait...they'll let ya know which is best.
Fall, i prefer to use large baits 10-14" and up to 2 lbs....late fall cut baits can be a good choice.
Like Jack, i too have found some years to be a fresh cut bait year, then years its only live...its not hard to get a pattern on the bait types(live or cut) or the specie of bait they want with experience.
You have to experiment on your water to find out. Like some of us, you have to put in years of fishing before you get consistant on flatheads...but everyone has an "off" season...or 2 if your like Jack(just joke'in Flathunter).
Scott