I'll leave the lengthy explanation to others that will surely come to help you out.
In the meantine, check out this tidbit on
pinch hitting.
Substituting on Offense (Pinch Hitting)
To insert a pinch hitter while you are the offensive team, drag a new hitter from the roster list on the top of the screen directly on top of the player you wish to replace in the lineup. Players in red have already been used in the game, and cannot be inserted as pinch hitters. The number of the player currently at bat is highlighted. Once you drag a player into the lineup, his position will be listed as 'PH' (pinch hitter). You can choose a position for this player now by using the drop-down. If you do not choose a position, you will be prompted to choose a position for the player at the end of the half-inning.
Just don't pick a position for the pinch hitter. At the end of the inning you will be told to pick your pitcher.