http://iscoresports.com/

My scorer did not put in the courtesy runner or mark a stolen base.

I went in after the game and subbed in the CR as a sub. (No CR option). However, I could not find a way to give him the SB.

To modify a statistic post game, go to Game Manager, select the game, in this case, you would select Batting for the team the runner is on, then tap the Stolen Bases value for that player, and add 1 to the value. Overrides done this way will be included in cumulative statistics as well.