The selection of whether a natural attack is primary or secondary is done when creating the race as far as I can tell. In D20, there is a checkbox. I did some digging in Pathfinder, and discovered that when you select the natural attacks, you can hit the button "Tags", add a new tag and specify:
Group ID: Helper and Tag ID: NatPrimary
There might be another way, but this one would seem to work.
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