I would not allow a ranger to select Multiattack as a bonus feat at 2nd level.
I would rule that Two-weapon Fighting only applies to manufactured weapons and unarmed strikes, so you cannot TWF with a manufactured weapon and a natural weapon.
If you attack with a manufactured weapon, all your natural weapons become secondary. You attack at a -5 penalty, and gain only 1/2 your Strength bonus to damage. If you have the Multiattack feat, your secondary natural weapon attacks only suffer a -2 penalty, but still get 1/2 Strength bonus to damage.
I would allow TWF to be combined with secondary natural attacks, and the TWF penalty would not apply to the natural weapon attacks.
I would rule that a creature only has one primary natural attack (except for special cases like the chimera). If it has a number of natural attacks that could be primary, it should pick one type to be primary and the rest would be secondary (a megaraptor skeleton, for example, has its talons as primary, and its claws and bite as secondary).
So, a bone devil ranger 2 attacking with its natural weapons would attack with a bite (primary) at +16, two claws at +14 each (secondary with Multiattack), and a sting at +14 (secondary with Multiattack). If it attacked with a longsword in one hand, it would be +16/+11/+6 to hit with the longsword (multiple attacks due to high BAB), and would get a bite, a claw and a sting at +14 (all secondary natural attacks with Multiattack). If it is using TWF with a longsword and a shortsword, it would be +14/+9/+4 to hit with the longsword, and +14 to hit with the shortsword, its bite and its sting.
