http://iscoresports.com/

When the opposing team tells me about a sub do I need to wait until the player being subbed comes up in order or is their a way to do it in advance?

You can bring up the sub screen at any time and do the substitution. Tap a fielder to do a sub on the current defensive team, and tap the batter to do a sub on the current offensive team.

Note: iscore manages offensive and defensive substitutions as two separate activities. If it is a full substitution, you have to make it both for offense Line up spot and defensive fielding position. (click the offense/defense buttons on top of sub screen to toggle back and forth)

Iscore does this because the idea is to score it as you see it..