Here are a few tips for newbies on organizing your minor leagues. Your goal is to have 5 viable teams that don't get overtired, and to develop prospects with potential.
Why is it important? To develop prospects properly you need to give them proper playing time, have them at proper positions, and give them orderly promotions. If they don't play enough or don't get promoted, then they won't develop. If they play too much and tire they are more likely to be injured and if you put them at the wrong position their defensive ratings won't grow properly.
Also, if you ignore your minors, you'll irk your fellow owners because it throws off the realism of the league.
To do list:
#1: Resign all of your minor league free agents. You'll need them and its easier then finding free agents
#2: Identify your key prospects. (The team depth chart under World Office: Reports is handy for this; sort by projected ratings) Who is projected to be major league quality or at least close? For a pitcher they should have a vs. R and control of at least 50, preferably 60. Like MLB, hitters are much more dependent on positions, if someone gets to recommended defensive levels at CF, 2B, SS, C, they can make the majors even with a weaker bat....but everyone else has to hit very well to make it.
#3: Promote key prospects. Development can be stunted by staying at the same level two years in a row, so if you see a potential future major leaguer, be sure he's not at the same level as last year.
#4: Check defensive positions. On your edit rosters page if you click on the defensive position (i.e. "2B") it will show you recommended fielding levels. Hit the "show recs (proj.)" button and save that. If your team wasn't well run, you'll have guys listed as SS and 2B who really have no business playing there. If I was taking on a new team I'd do this for everyone in my system, but at least do it for key prospects.
#5: Assign your "needing assignment" (resigned free agents) guys where it looks like they will be needed. See below for what is needed.
#6: Promote your "non-prospect" prospects a level if you need them at the level above.
#7: Clear out Rookie League if you need them at higher levels. Rookie League doesn't start 'til after the draft so you can empty out your roster down there if you need fillers.
#8: Sign minor league free agents to fill spots.
At the end, your goal should be to have the following:
AAA and AA: 1 per defensive position + 3-5 subs (at least 1 of those needs to be a C and 1 should be able to play SS). 13-15 pitchers, at least 5-6 should have stamina at 65 or so plus so they can start. This many players means you should start with a couple inactive players, who should be the weakest guys.
HiA and LoA: 1 per defensive position + 4-6 subs (especially C and infield). 14-17 pitchers. You should have 2-3 inactive pitchers at all times...you'll need them during the year when your guys tire and get hurt. You need more guys at A ball since stamina is lower and injuries more frequent.
Any questions? Post them on the chat board or ask a veteran.