I spent a good number of years running a bass boat on Lake Erie. I don't get much rougher than that old lady
I recommend a 4-blade prop setup. Second, if you don't have one, I much prefer a HotFoot throttle. Trying to control boat speed with the hand throttle in really rough water ain't my cup of tea. I prefer BOTH hands on the steering wheel
Running in "following" waves (going with the wind instead of into it) is, to me at least, tougher than running into it. A couple of days ago, I had to make a 6 mile run back to the ramp in 20mph winds in the following waves. Not the smoothest ride I've ever had : If I'd have been running into them I'd have had a much better time of it.
If the waves are running close together I normally put her up and let her run. Keep an eye out for those sneaky bigguns that crop up. In swells it's time to slow things down a bit.
One thing I do if I'm fishing Kentucky lake is to check the Intellicast page on the internet for the wind forecast, and make my early AM run so that when I return, it's always INTO the wind. With a direct wind from the North or south, that body of water can darn near equal anything Lake Erie can toss at you at times.
Seat time will improve your rough water handling. Just remember....KILL SWITCH AND LIFE JACKET....ALWAYS.