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I manage my minor league systems myself except line-ups. When I start a new MLB game I first check my Minor League system and put all players at the correct level.
This is a bit of work at the beginning but you also get to know your Minor Leagues right away. When setting up the rosters for each team I make sure I have more then 25 players on the roster. My rosters look something like this: 15 pitchers (7 who can start), 2-3 C, 2-3 1B, 6 IF & 6 OF. Each of my teams will have about 30 players on their rosters (including short term injuries, excluding long term injuries) and I try to have each position covered 3 times (3 different players who can play C, 3 different players who can play 2B etc.)
The main problem I ran into in he past was injuries. When you have 25 man rosters you constantly have to move players up and down to cover for these injuries.
Not only is this a lot of work, but moving players down also affects their morale. If you carry more players on your rosters like I do, you don't have this problem. For the most part you have enough players to cover for injuries.
For the rest you should treat your Minor Leagues as a breeding ground for prospect. Focus on them and their development. The rest of the players are just warm bodies to feed the prospects. Make sure all your prospects are at their correct levels and promote them when ready.
If you have to move player up a level to cover for an injury, do not use a prospect for this but one of the scrubs. Only promote a prospect when he's ready. Also make sure the prospects do not get in each others way. If you have 2 catcher prospects, make sure they are on different teams. Finally make sure your prospects get experience at different positions. If a OF prospect only has experience in CF, force start him at LF and RF for periods so that he gains experience there.
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