I’m afraid that’s my experience with S4S, too. It is never flat. When I use S4S, I have a notion of my cut list and I site the boards in the rack trying to see reasonably flat sections from which to take my pieces. If I can rip down the middle of the cup and take pieces from the two sides, that can greatly reduce the cup.
The second level of frustration is that, once you cut to size, the wood is likely to move again, especially twist and cup. So, you need to leave some extra material on, which may mean not getting perfectly flat. In other words, you get close to dimension and close to flat, then let it sit at least overnight and then get a bit closer. You’ll have a sense of whether you need to do that a second time or not based upon what you see. Of course, before doing any of this, let the wood sit in your shop for some time to equilibrate.
Once you have the material to dimension, put it in a thick plastic bag and keep it there other than when you are working on it. Don’t let it sit out. Maintain that until you’ve glued up.
Honestly, rough sawn is going to be the same, but there are two big differences. First, once you find a good lumber yard, the material will likely be dried better than what you find at box stores. Second, you will have extra thickness so that you can end up at your desired dimension. If you start with S4S “1-by” material, you will almost certainly not get 3/4″ out of it for many pieces. With hand tools, that doesn’t matter so much, luckily. And, it goes both ways: If you get rough sawn 4/4 and your plans call for 3/4″ thickness, think about whether you _really_ need to be 3/4″…maybe you can just get to flat and true, which will be more like 7/8, and go with that rather than hogging off all that extra material by hand.
When you do finally find a lumber yard for rough sawn, keep in mind that many of these places will be happy to do a “quick jointing” of one face and maybe a “skim plane” of the other. They do this because many builders want to see the grain and color. For someone with hand tools, this can give you a _huge_ head start for dimensioning. But _watch_ them. Some places will do the “quick jointing” by jamming the rough sawn into the planer. That is worse than useless. Say no thanks and go somewhere else. Others will actually take a few passes over a jointer (often an unbelievably BIG jointer), then a pass or two through a planer.