Good question and tough one. You're likely going to get a variety of commentary on the subject. Mine's, for the most part, pretty simple. Do what your gut tells you.
You can methodically do it all manually, or you can delegate the chores to your AI minor league managers and then monitor, making changes as you deem fit. If you haven't read the "Fundamental Flaw" thread, although it doesn't directly talk about your issue, it still contains some awfully good thoughts about minor league management.
In my case, for instance, just starting a new league, I have a couple players who, by all rights, should be in the minors after Spring Training: good prospects with great potential, but lacking existing overall tools right now. Regardless, it's my plan to keep at least one of them on the bench to acquire some ML experience and that probably cuts against the traditional grain of wanting only ready-now players on the active roster.
Who's ready now? You can look at stats, ratings, overall/stars, green or red arrows (will be working better in the next patch), how much room for growth and playing time the specific player can get at his current level (are you blocking him, for instance), or just take a classic go-from-the-gut approach and figure you'll either know it when you see it or roll the dice and take your chances. You'll have to decide how much management or micro-management you want to take on and that, of course, can change as you grow in the game.
