I am only inputting specific campaign rules in the mechanics section. So I am running Skull and Shackles which is a pirate campaign. I have our ship combat rules, sailing information, ship types, weather effects, and other Unique Rules I need for this campaign. I also have any other "special" houserules for this campaign.
Everything else like normal spells and monsters or diseases are referenced from d20pfsrd. I see no reason to enter the information twice when its already in a giant wiki database.