Later in the game...
I've never seen a game where at least one substitution was not made. There are many reasons to replace a starter: pitchers get tired, batters aren't hitting, players get injured, someone's ejected, or the manager makes a strategic move. Whatever the reason, sooner or later you're going to have to mark a substitution on your scorecard.
So, how do you do this? It depends on the substitution.
For batter substitutions, I draw a line between the last scorebox of the previous batter and the first scorebox of the new batter.
Kitt pinch hits for Lawson
If the new batter is a pinch hitter, place "PH" in the position box. If he is taking a position in the field, use the normal position numbers. If players are moved around in the field, you'll want to show that on your scorecard. Usually, I make a note by the player's name indicating the move.
When a substitution is made for the pitcher, place a line under the score box of the last batter the previous pitcher faced.