Pfs and reputation
 

I have earned reputation for multiple PFS factions and I am have trouble working out how to add the reputation the secondary faction. Any help would be nice.

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.

Also, on the profile tab, make sure the second faction has been added to your faction list, so that HL has somewhere to store the amount added.

The last point is a bit confusing for some, as one has to add factions that they do not have a Boon for. It is a moot point for the restructure of the factions and removal of Fame, but you can add a faction to choose from in the profile section without having to "buy" the champion boon. I had to have this pointed out to me when I was fighting with it a bit ago.