This subject is covered in the user guide, but quickly...
In the Game Planning view (full view of players and positions), each inning number is a button. Touch the inning number and a display of players in order and by position.
In this view simply touch the drag control (small 3 line 'button') at the far right of each player line, and then drag the player into the order you wish them to bat.
Batting order is only set for the first inning so the 1st inning is usually selected but... you may change the order from any inning you wish.
This is especially useful when batting 9 or 10 because you are able to drag the players out (marked with an 'X) to the bottom of the order, and then make refinements after that.