I believe there are options that can put you in charge of certain things with the minors and the coaches in charge of others. Right now I have my minors completely managed by minor league coaches because I did an inaugural draft and got no prospects.
As soon as I do the draft I'm going to stop them from being able to promote and demote, and stop them from signing/releasing. Mostly I had nobody on my A team and I didn't want to weed through a billion no-name no-talent hacks just to field a crappy team.
Regardless, you can make it so they can't promote/demote or sign/release if you want. Then the computer will take care of the lineup, but you need to make sure you have the right guys there. You can also force certain players to start but I don't know how that works.
A lot of people use ghost players so that the only guys in the minors are the ones that mean something to you as a ML GM.
At some point I assume I will descend into madness and control the lineups in the minors.
Good luck!
I'm new at this so I don't have much advice for you yet. But I've had trouble getting into the season - after the first couple games it'll be easy though.