Warpriest Favored Weapon and Sacred Weapon
 

I am trying to find out is I am missing a setting, adjustment, or option for Warpriests.
Sacred Weapon says: "In addition to the favored weapon of his deity, the Warpriest can designate a weapon as a sacred weapon by selecting that weapon with the Weapon Focus feat"

Yet only weapons I have selected with Weapon Focus appear to be affected by Sacred Weapon. This is coming up with gods that have Bite as their favored weapon, though I have not sat down and tried to test it with manufactured weapons(as opposed to the natural ones I ran into the issue with). Is Weapon Focus the only way to turn on Sacred Weapon in the builder? Or is there a way to emulate it without adding in the extra attack bonus from weapon focus?

Edit: For clarity, the wording indicates that the favored weapon is always affected by Sacred weapon and that additional weapons can be affected. I meant the extra attack BONUS granted by focus weapon. as this could come up with a dual wielding level 1 character with two different weapons, a deity's favored one and a Weapon Focus selected one, on my case Claws with Weapon Focus and what should be a Bite from Apsu's favored weapon.

weapon focus doesnt grant an extra attack,

As far as I can see, this works correctly in HL. Any weapon I have picked (if it matches the deities favored weapon) gets its damaged correctly modified. You don't have to have weapon focus.
Most heroes do not have a bite attack, and I've never seen a deity with a bite attack as favored weapon. In any case, natural attacks (like bite) are not weapons, so there is no reason for a Warpriest that did get a bite attack to have Sacred weapon function.

Natural attacks are weapons. They are enhanced via the amulet of mighty fists, and similar. The effects of natural weapons and manufactured weapons are called out when used together too.

Thanks Minous - I'm corrected - I didn't read enough on natural attacks.
On that basis, Xeth, if you have a Warpriest with a deity that has bite as favored weapon, and your hero has a bite attack, then the damage should be adjusted to match the Sacred Weapon. If you don't see that happening, then report it as a bug.

I just created a deity in the editor with bite as his favored weapon. Then started up a warpriest with that deity. The bite damage increased from 1d4 to 1d6, so it appears to be functioning correctly.

It sounds as though your thinking is that the sacred weapon grants an attack bonus - it does not.

e.g.:

Warpriest worships deity with Warhammer favored weapon. Warpriest takes Weapon Focus: Light Shields.

Attack with Warhammer is at +0, but gets increased damage from Sacred Weapon. Attack with Shield Bash is at +1 (from Weapon Focus feat) and gets increased damage from Sacred Weapon.

Maidhc,

That was how I understood it to work as well, but it wasn't scaling the damage on the bite attacks after I selected claws with weapon focus. It would scale the bite only when I selected it with Weapon Focus. I hadn't tested it with manufactured weapons rather than natural ones, or gods that only hav one favored weapon. I also want to test the Cult Leader archetype because they trade away weapon focus at level one. I just hadn't had a chance yet.

It does sound like there isn't an individual adjustment or toggle I am missing though, which is good. So Favored Weapon should work even without Weapon Focus.