The eidolon totally gets iterative attacks with a manufactured weapon when its base attack bonus is +6 or higher. From here...
Base Attack Bonus (BAB): Each creature has a base attack bonus and it represents its skill in combat. As a character gains levels or Hit Dice, his base attack bonus improves. When a creature's base attack bonus reaches +6, +11, or +16, he receives an additional attack in combat when he takes a full-attack action (which is one type of full-round action—see Combat).
...and here...
Base Attack Bonus: A base attack bonus is an attack roll bonus derived from character class and level or creature type and Hit Dice (or combination's thereof). Base attack bonuses increase at different rates for different character classes and creature types. A second attack is gained when a base attack bonus reaches +6, a third with a base attack bonus of +11 or higher, and a fourth with a base attack bonus of +16 or higher. Base attack bonuses gained from different sources, such as when a character is a multiclass character, stack.
Undoubtedly there are edge cases wherein a creature using a manufactured weapons doesn't get iterative attacks, but such a feature would be noted among the creature's abilities.
Natural weapons for the most part don't yield iterative attacks. Instead, the creature uses one natural weapon during a standard attack, or all its natural weapons on a full attack, with some natural weapons designated primary and other natural weapons designated secondary as per this chart; secondary natural weapon attacks suffer a -5 penalty to attack rolls and the damage bonus from the creature's Strength score is halved.
A creature wielding a manufactured weapon that also possesses natural weapons who takes the full attack action attacks with his manufactured weapon normally (including iterative attacks due to base attack bonus and usual damage bonus due to Strength) and can also make natural weapon attacks with any natural weapons not occupied with the manufactured weapon, but all such natural weapon attacks are considered secondary, suffering a -5 penalty to attack rolls and the damage bonus from the creature's Strength score is halved.
A cursory search should reveal questions probing the use of natural weapons in Pathfinder and its precursors and get answers that go into staggering detail.
There are no rules regarding over-sized weapons and using more than two arms. Normal over-sized weapon penalties apply.
Inappropriately Sized Weapons: A creature can't make optimum use of a weapon that isn't properly sized for it. A cumulative –2 penalty applies on attack rolls for each size category of difference between the size of its intended wielder and the size of its actual wielder. If the creature isn't proficient with the weapon, a –4 nonproficiency penalty also applies.
The measure of how much effort it takes to use a weapon (whether the weapon is designated as a light, one-handed, or two-handed weapon for a particular wielder) is altered by one step for each size category of difference between the wielder's size and the size of the creature for which the weapon was designed. For example, a Small creature would wield a Medium one-handed weapon as a two-handed weapon. If a weapon's designation would be changed to something other than light, one-handed, or two-handed by this alteration, the creature can't wield the weapon at all.
The rest of this answer assumed multiple greatsword (or other two handed weapons).
You cannot use the Two-Weapon fighting feats if you are using more than two arms. You need to use the Multi-weapon fighting feats. If you were fighting with two greatswords, one of them with be primary, the other offhand. Likewise, if you had sixarms, two for the weapons would be offhand, and so on. You will always have one primary weapon.
Multiweapon Fighting (Combat)
Prerequisites: Dex 13, three or more hands.
Benefit: Penalties for fighting with multiple weapons are reduced by –2 with the primary hand and by –6 with off hands.
Stealing the table from this answer you would make your all your attacks at -4 regardless of if they were off-hand or primary:
Table: Multi-Weapon Fighting Penalties
Circumstances Primary Hand Off Hand
Normal penalties –6 –10
Off-hand weapon is light –4 –8
Multi-Weapon Fighting feat –4 –4
Off-hand weapon is light and
Multi-Weapon Fighting feat -2 –2
I have found no rule which changes the damage modifier (*1.5) from high strength.
Likewise, power attack applies to all attacks as described, there are no special rules for using more than one two handed weapon. The primary great sword would get +3 per -1 penalty. The off hand greatsword would get +1.5 per -1 (rounded down, so +1, +3, +4, +6, etc. )
Emphasis all mine.
BONUS HOUSERULE:
I would not allow a creature to use a weapon who's category was more than two handed, as per the normal rules. However there are items in 3.5 that required more than two hands to use ( I think it was the scissor sword ) and had better stats.
I would also allow a creature with more than two hands to substitue the Multi-WF feat in place of the T-WF for classes with bonus feats, such as ranger.
Have a look at the Gythka and Scissors Sword, which are four handed and six-handed weapons from Savage Species (I know, not pathfinder) on page 45.
Best Answer
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