Once you simulate you hand over captaincy to the AI. You'd need to sit there playing in real time to be able to have total control.
It's been discussed in the past about having some form of match tactics options, letting you get your AI controlled players to do particular things (bat for a draw, smash it around, focus on economy in the field, etc) but that's almost certainly a next edition thing rather than a patch feature.
ah ok, maybe an interim step to decide what the AI can have control over whilst simulating would be good.
So tick boxes for Change bowlers, set fields, batting order, declaration.
AI then would only change things you let it decide on, so if i'm captain and dont set any AI orders then things continue as they re until i change something.
Also think the AI needs a bit of tweaking, surely no one would declare on a 250 run lead with 4 wickets down at tea on the 2nd day of a 5 day test match (weather dependent i guess), most captains would keep batting for at least another session or 2 and bat the opponents out of the game!