Position player fatigue I have deduced comes from a formula that seems to work for me. 730 * durability% = plate appearances per season. That is not AB's by the way, you need to look further into reports to finds a players PA. Position fatigue happens when the driver determines that a players PA's will exceed the point by the end of the season. Batting order also needs to be figured in BTW, top of the order will have more PA's.
Resting a player recovers the below 100% of course. Once a player gets below the 100% barrier can be tricky to keep him there. Best way is to get him back to 100%, then play him 2 on 2 off for about twenty games. All-Star break can be very helpful in this aspect as it is considered three days off for everyone. A player recovered at that time usually doesn't have a problem for at least ten games before it starts again. There have been cases where a player has exceeded the formula and never went into fatigue even with low durability. That happened a few seasons ago and that problem was resolved.
Durability above 88 rarely runs into fatigue issues. Below 80 is where it starts becoming problematic the most.
Best way around the problem is rest a player at least one game in every ten for 75 and above. Two games for 75 to 65, the rest need careful watch.
There are ways around the fatigue issue but becomes very taxing. For instance a 40 durability catcher can be in all 162 games and start 60 of them and exceed 300 AB's but you have to watch him carefully.