Are you talking about the bonus faction reputation some scenarios earn? In the journal, there is a dropdown for 1st and 2nd reputation awarded—these are a little misleading, because they are both for bonus reputation.
The amount you put into the Fame and reputation awarded field is the scenario reputation, and is applied to whichever faction boon you have slotted. Then at the bottom of the journal, there are fields to enter the amount of reputation for bonus factions selected in one of the dropdown menus.
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