I have vertigo in one of my ears, so turbulence affects me pretty bad to a point where I can get really dizzy and feel like I am spinning. I try really hard to fly in a window seat because it helps me to look out the window and see the horizon. I have flown many times on the regional jets over the years and have found them to be no worse than the larger jets. Like people said, the best thing is to fly early in the day before afternoon warming. And crossing the edges of mountain ranges, like in Colorado, can be really rough. I avoid Phoenix and Vegas in the afternoon in the summer as you get the worst of both together. As far as turbulence in-flight, longer flights usually have an easier time taking routes that avoid turbulence, whereas short flights can't go as far out of the way. If weather gets really bad, there is a greater tendency for them to cancel the regional jets, but in that case, at least you didn't have to fly in the bad weather.
If it were me, I would take the regional jet, and get a window seat over the wing if possible. Good luck!