Hate to agree with Diesel, but I still reread that book from time to time. Other random comments...

I play WITH the warmup rule on. Yes, it's a bit of a disadvantage, since the CM doesn't have to follow it, but I like the extra bit of strategy it adds. I also control baserunning and throwing, and the biggest thing to keep in mind is to be conservative. As a whole baseball simmers are A LOT more aggressive than real life coaches.

As for pitching, the other guys have pretty much nailed it. Watch the pbp and results to try to get a good read on if a pitcher is fatigued. Watch his pitch count, not only for the current game, but for the past few days. There is a chart in the help somewhere that gives the different ranges for around when pitchers will start getting fatigued.