You can give bonus points and penalties to every team in your championship.
To do so, click on "Stats > Standings" and finally on "Edit bonus points". You will therefore have to choose whether you want to give them bonus points or penalties and enter a reason for giving them (if one exists).
Let's take an example!
Here is the final standing of the Paris FLA D1 Championship:
But, you need to subtract 3 points from the Olympiens FC who were found to have cheated and 2 bonus points to Montrouge 92 FC, who were the victims in this case.
So you do the handling explained higher:
And thus, this will be the final championship standing after the bonus and penalty attributions: