[Pdubya64]

You need to check under Organization/Minor Leagues for an overall look at each of your minors teams.

For each team, to the right of a player's name is a small "block" with horizonal lines; here is where you have most likely already seen a RED down arrow or GREEN up arrow. This is the Minor AI telling you what it thinks of a given player's position relative to his talent/readiness level.

You can also go up to the top right ACTION and the bottom choice from the pull-down menu is "Have AI configure Minor League teams only" (something close to that, I am not in the game atm). This will give you a decent baseline if you are just starting a playthrough.

A side note; you will find that certain levels in the minors (typically A to A+, but it can vary) will have LOTS of players with RED arrows. Unfortunately, you need as close to the 26 player limit as possible, so watch your number of players at each level so the team can actually play games and have enough guys on the team at the right positions.
You will get the hang of it after a while. Note that when you sign free agents they almost always appear in one of your lower R or Dev. leagues. You will need to remember to check right away, look for the telltale GREEN arrows. You can hover over a player name to pull up his quick chart and see the level of league(s) he has or was last in (cutoff by box size at times). Then I will start advancing him up the levels until the GREEN arrow goes away.

As you can see there is quite a bit to it, but it isn't too difficult. Also, know that having minors Hitting and Pitching coaches and Head coaches who aren't terrible has a direct influence on minor league players learning and advancing their skills.

Good luck!