Summary: Player fatigue is more complex than just benching a player every few days. You have to manage playing time to control player fatigue on both a day-to-day and a season-long level.
Baseball players generally suffer from two types of fatigue: the day-to-day (short-term) fatigue, and the seasonal (long-term) fatigue.
Generally, all fatigue is a factor of a player's Endurance. Each player has a "maximum Endurance" (the rating you see) and a "current Endurance". Fatigue is a player's Current Endurance (cEN) divided by his Maximum Endurance (mEN). As a result, a player who is fully rested (cEN equals mEN) is at 100%.
All players lose a similar number of Endurance points when playing. As a result, players with higher overall Endurance will fatigue more slowly than players with lower overall Endurance.
'Example:' Player A: mEN = 80, cEN = 80, Fatigue = 100% Player B: mEN = 40, mEN = 40, Fatigue = 100%
After both players play a single game, and both players lose two "Endurance" points:
Player A: mEN = 80, cEN = 78, Fatigue = 97.5% Player B: mEN = 40, mEN = 38, Fatigue = 95.0%
As you can see, both players suffered the same endurance loss, but because Player A has a greater overall Endurance, the effective fatigue he suffers is less than the less-durable Player B.
Position players fatigue is based on how much playing time they have in a game. They generally lose 2 to 4 points of Endurance in a typical game. Designated hitters generally lose about 1/2 the fatigue of non-DHs (1 to 2 Endurance points lost per game), and catchers generally lose about double the fatigue of other position players (5 to 7 Endurance points lost per game). In addition, a non-catcher playing catcher will suffer additional fatigue after each game (an additional 2 Endurance points lost per game).
Pitchers lose fatigue based on pitch count. Whereas players lose a little fatigue each day, pitchers may lose a lot of fatigue in a given day (especially starters). As a result, pitchers need more rest to get back to 100%.
Each day off, a player recovers 1/3 of his maximum Endurance. So, a player with an Endurance of 60 would recover about 20 points of Endurance after a day off. As a result, any player - pitcher or position player - generally will return to 100% after three days rest, 'provided their fatigue did not go below 0%'.
In all cases, players do not suffer fatigue penalties until their Fatigue falls below 50%. At 50%, players begin a steady decline in their ratings until 0%, where their ratings are reduced by 20% (10% for pitchers). Below 0% comes a more accelerated decline; players who reach -50% fatigue would be playing with their ratings reduced by 50% (40% for pitchers).
There are a few ways keep your players rested, aside from manually adjusting lineups between games.
A full baseball season can take its toll on a player. Players have limits as to how much they can participate in a season before they start suffering long-term fatigue penalties
How much a player can play is based on a factor of a player's Endurance. Players with the bare minimum Endurance (1) can play in about 50% of a team's games before suffering any sort of long-term penalties. Players with a high endurance (over 90) can play in nearly all of a team's games without issue.
Season fatigue can set in early or late in the season, depending on overuse of the player. The impact of the season fatigue depends on how overworked the player is and how long the player has been overworked.
'Example:' Player C has an Endurance of 50, which allows him to play in about 75% of his team's games without adverse affect. Twenty games into the season, he's played in all 20 games. This is over the 75% limit, but since it's only been 20 games, the impact is small (if not nonexistant). However, if the player continues the pace the impact of season fatigue can grow.
You can offset season fatigue by resting a player to get him closer to his physical limits. If Player C from our example played 80 out of 80 games, he would be suffering some season fatigue, as he's played in 100% of his team's games halfway through the season (compared to his reasonable limit of 75%). However, if he played in 20 of his team's next 40 games, bringing him to 100 out of 120 games played, his season fatigue would have gone down. He still is overplayed, but now he's played in 83% of his team's games
Season fatigue can be very small or very dramatic, depending on the Endurance of a player and how much he is overworked. Most players with reasonable endurance will be able to play in the majority of their team's games with minimal impact.
Note: Each game at DH causes less potential season fatigue than when playing a position. Toggle your use of designated hitters to extend low-endurance players.
Whereas day-to-day fatigue reduces a player's current Endurance (which is a factor of overall fatigue), season fatigue impacts two things:
1. How much a player recovers in each day of rest. If a player is suffering season fatigue, the amount of Endurance he recovers with a day off (normally 1/3 of a player's Endurance) will be reduced, based on the extensiveness of the season fatigue. 1. A player's maximum overall fatigue. A player who is suffering season fatigue would have his maximum Fatigue capped at a certain number. As a result, players may never be able to reach 100%
The formula for season fatigue is complex, but takes into account a player's usage as compared to how far into the season it is. Players can be used lightly at the beginning of the season and play hard at the end to avoid suffering season fatigue; similarly, players can be rested at the end of the season to get themselves a little extra rest (and less season fatigue) before the playoffs.