When a team forfeits a fixture, you still have to enter a score for that fixture. You do this by editing the details of that fixture, checking the "Fofeit" checkbox for the team that forfeited, and entering a score in favour of the team that did NOT forfeit.
What happens then is:
The system allocates however many points are specified in the league details screen for a win to the team that didn't forfeit
The system allocates however many points are specified in the league details screen for a forfeit to the team that DID forfeit. This can be a negative amount
If you want to then make it so that the team that arrived doesn't get actually get awarded any points you can create negative bonus points for that team. Similarly, in the "View/Modify Standings" section under "Divisions/Teams" for the league you can manually modify the number of runs scored for the team that did not forfeit to remove the runs that you had to add when saving the fixture.