From what we know you can play everything ball-by-ball if you want or skip to "events" that you're a part of. That's as a fielder, bowler or keeper. Other than that, I guess lets just wait and we'll find out when the game is out. I don't really think it's something we need to delve too deeply into thinking or discussing to be blunt...
We can reasonably assume in main game, the keeper will have some base-level of autonomy (catching the ball, etc) and you will control your fielders. Again, see the MLB video posted to get an idea of where they're going with that stuff as I think that is the inspiration for how BigAnt have their game set up.