The basics that most good owners I've talked to follow is -
Make sure prospective BLers are at the appropriate level based on age and level of talent.
Make sure they play as much as they can. 'Play' is not necessarily tied to IP or ABs. Its tied to games played.
Make sure that they are (usually) promoted each season (Unless they are horrible and at a higher level than they should be). Multiple seasons at the same level will stagnate their development.
Keep your training maxed out. Set it to $20 million and forget about it.
Keep your coaches in the 'top 10' level for their relevant ratings. You can get this by running a coaches report for previous seasons. (Always keep an eye out for some leagues where owners over-promote coaches to save money. Average ratings there can be misleading). If you can afford to have the best at every level then go ahead, but generally that money can be better used elsewhere. Whats the difference between a pitching coach with a 74 vs a 70? I'm guessing it isn't a huge difference.
A few other things that (can) help out -
(Note: Not all of this is proven)
Don't play trash catchers in the minors. I try and stock catchers that have excellent throwing and pitch calling - even if they can't hit. Why? Because your minor league pitchers will - theoretically - pitch more and get hammered less.
Make sure you play minor league players in the correct positions, and aim to have good defensive players out there. Why? Again, that only helps your pitchers out. Having a DH at SS isn't doing your pitchers any favor.
I usually don't want my best position prospects replaced by pinch hitters or pinch runners, so I turn that off for them. I do want them to rest however.
As Mike has said before, do your due diligence in drafting, follow the advice in this post, and then forget about those guys. Where they end up really won't be apparent until 3-4 seasons from now. That's a whole year. Plus, advanced, unless its near or at max, won't tell you sh1t about where a player will accurately end up. Plus a player can get wacked with an injury. So just do your due diligence and worry about them later.