http://iscoresports.com/

My league has a 6 run rule per inning. My team had scored 4 runs already and had 2 on when the next batter hit a HR. All but the last run should count. Is there a way to have the HR count in stats but not the run or RBI for the last batter. I can't make the run not count when I click HR button after Clicking the in play button

You should mark the runners before the home run as Run Not Scored. You can not enter a Home Run for a batter and not count his run.

Will there then be a way to alter the stats later that essentially lets me take a run scored off one player and add a run scored to another so season stats are corrrect, thanks

Yes, you can override the stats. Go to Game Manager, select the game, select Batting Stats for the team, and tap any non-bold field to edit the value. (The bold stats are calculated from other fields).