Once you control the things you can control, the rest is out of your hands.
I'd focus on evaluating your team in every single spot. The close games are going to be won by pinch hitting, poor/great baserunning, relief pitching and defensive replacements. Your manager settings are key, but if you don't have the horses to take advantage of late game manager settings, then the settings themselves are moot. In my opinion, an NL team should look for one or two solid guys that can play every day then load up on platoons every where else. Pinch hitting is huge in the NL so if you have some league average pitchers, put a bit higher pull rating on them so they can be pinch hit for if needed.
I like to have a basher vs. Lefties on my bench while facing a right handed starter and a basher vs. Righties on my bench while facing a left handed starter. This gives the Sim incentive to use pinch hitting. Also, whichever C is the better defender, be sure he is set as the defensive replacement late in games. Any backup SS with great defense also needs to replace middle of the road defenders at 2b, CF or 3b where applicable. And make sure that poor hitters are set to be pinch hit for and great hitters are set not to be pinch hit for. Also, if you have poor hitting Fielders, make sure they have a defensive replacement behind them so they can be pinch hit for. You can turn off their personal checkbox to be replaced in player settings so they won't get replaced defensively, but if there is nobody in the defensive replacement setting for that position, often times, the Sim won't bring in a pinch hitter.
Also, don't run into outs. I use a rule of thumb that has helped me out consistently. If you have a guy that gets on base 34+ percent of the time and his baserunning +speed is over 150, bump your basestealing settings up one notch. For every guy that fits this criteria, bump the settings up one notch. I rarely have it above the average setting because I rarely have multiple guys that fit the above criteria that also play every day.
And make sure to use judicious rest. If you are losing or winning a game by five runs, have your lower durability guys get some rest. Another thing that leads to unnecessary losses are fatigue and injury.
The rest of it is up to run distribution, the timing of simulation's implementation of your settings, hot and cold streaks, seasonal player performance variance, etc.