If a player is absent on an Individual Player League, you can either choose a sub for that player by clicking the player's name when you enter scores, or if there is no sub, choose "Absent: The Course..." from the drop down list and the "course" will play for the player.
When you have a 2-player team league and a player is absent, you have 3 options:
When a player is absent, the "Course" plays for that player by choosing "Absent: The Course..." from the player drop down list on the score entry screen. Think of the course has a real player with a 0 handicap, who makes a par on every hole.
You can also penalize the absent player with a setting in the system called "Absent Player Penalty Strokes". This setting makes the course have a negative handicap of whatever value you set, which effectively makes it so the course is shooting that number of shots over its handicap. If you were playing match play, and a player with a 5 handicap is playing against the course, and Penalty Strokes are set to 2, the Course Plays as a -2 handicap. This means the player will receive 7 strokes because the difference of his handicap and the course handicap is 7 strokes (5 minues -2 = 7). This player will get 1 shot on the 7 hardest holes. The net score for the course will also be Par minus the Course Handicap.
For points, the absent player will receive whatever points "the course" wins... or in other words, whatever points the real player didn't win. You can limit the number of points an absent player can win in your league settings if so desired.