http://iscoresports.com/

Had a couple scrimmages lately where a kid had to leave in the middle of a game for other commitments. My scorekeeper used the "skip" at bat button thinking it would just skip to the next batter but it COMPLETELY screwed up our book. What is the right way to do this and not mess up everything?

Using Misc -> Skip Batter is the correct way to skip a player. That should not mess up your book. What would mess up your book would be to remove the player from the lineup. What happened when you used Skip Batter?

He said that it was showing the wrong player up to bat so he had to do a substitution for every hitter the inning she left. But it's got just about everything messed up on our hitting stats because it has the wrong players up to bat throuout the entire game. And the kid left in the fourth inning

It does not sound like Skip Batter was used correctly. If you have this lineup:

1. Player 1
2. Player 2
3. Player 3
4. Player 4
5. Player 5
6. Player 6

And you use Skip Batter on Player 3, everything else will stay intact. When Player 3 comes up the next time around, on an iOS device, it will ask if you want to skip that player again.

Sounds like the original batter was removed from the starting lineup (misc-starting lineup) rather than skipped (misc-skip batter.) Removing a batter from the lineup will screw up all the stats and the batting order for the entire game.