Your question is a little confusing.
Are you asking "Would the elemental rage, and if the extra damage would apply to all attacks, even those by both held weapons?"
Answer is yes. I would highly suggest the beast totem really, pounce is indispensable as moving with multiple attacks actually does a LOT with TWF.
say i was level 6 with 20strength
i would have +11 to attack -2 for TWF = +9if i had the Fiend Totem, Lesser. would i get +4 to attack with horns or +6 to attack with horns since my full BAB is +6?
and it will benefit from extra damage from elemental rage, lesser, right?
I agree about this being worded confusingly. If this doesn't answer your question, please restate it:
Yes, if you were level 6 with 20 strength, you would have attacks at +9/+9/+4 (with an extra /+4 if you had improved TWF).
If you had natural attacks (like the horns) and you attacked at the same time as you used a weapon (TWF is irrelevant here), you would attack at {your full BAB +STR -5}, which would be +6. If you were only attacking with the horns, and not attacking with a weapon, your attack would be at +11 (because the horns are primary natural weapons).
Lesser elemental rage adds 1d6 to all melee attacks. It doesn't matter if that means one greater vital strike'd attack with a Large bastard sword, or seven attacks from two weapons plus three natural weapons. Each time you attack someone in melee, you add 1d6 elemental damage.