Hit and Run Tendency refers to your SimManager's use of the Hit and Run. 5 means you want to hit and run as often as possible. Use this setting if you have a lineup of good contact hitters. 1 means that your team will very rarely ever hit and run. Choose this setting if you have alot of high strikeout hitters in your lineup.
Base Running Aggressiveness setting controls how frequently a team attemps to stretch a single into a double, a double into a triple or score from second on a single.
Intentional Walks setting controls the frequency with which opposing team's batters are intentionally walked. A less aggressive setting will rarely intentionally walk a batter, odd to fill first base with a man on second and one out. A more aggressive setting will walk power hitters with the bases empty and no outs.
Pinch Hitting setting controls how frequently a hitter will be pulled for a bench player. This includes pinch hitting for position players as well as pitchers.
Pinch Running setting controls how frequently a runner will be pulled for a bench player. This includes pinch running for position players as well as pitchers.
Double Switch setting controls how frequently a double switch is used to change the batting order and ensure a pitcher won't be hitting soon.
Defensive subs if winning by X or more runs in Zth inning or later allows you to specify how big the winning margin must be and how late in the game before your position players will be replaced by superior fielders on the bench, e.g. your team is winning by 3 in the 9th, should your current SS be taken down in favor of a slick fielding SS on the bench?
Rest players if up/down by X or more runs in Zth inning or later allows you to specify how big the score differential must be and how late in the game before your starting position players will be rested in favor of players on the bench, e.g. your team is winning by 6 in the 8th, should your starters be rested?
Only use closer(s) in save situations indicates whether you'll allow or not allow your closer to see action in a non-save situation where the score is tied, e.g. game is tied at 3-3 in the 9th, do you want your closer in or not?
Only use mopup pitcher(s) when losing indicates whether you'll permit or not permit your mopup pitcher(s) to pitch in a tied or winning game, e.g. your team is winning by 7 in the 6th, do you want your mopup pitcher in the game?