http://iscoresports.com/

Is it possible to edit the lineups as a game is being scored when using MLB rosters (or other for that matter)? For example, when starting to score a game, I may not have complete linups set yet for both teams and want to simply add each player as he appears at bat but I don't see any way of doing that other than substitutions.

You can go to Misc->Show Starting Lineup to add player... but be sure to do it before the next batter comes up (i.e. look in the on deck circle and add him at that time).