Are attacks with the primary hand considered primary attacks? Are primary attacks made with the primary hand? Are these two questions like a venn diagram where sometimes they are not the case?
They always match up the same.
Do you mean main hand and off hand versus primary and secondary natural attacks?
No, those are completely unrelated subjects. Your off hand is not just some substantially weaker limb, it is just the nature of balance for TWF and maybe due to the typical difficulty of swinging two metal objects around with coordination leading to a slight preference (a lot of power comes from the hips, which might be used to handwave the effects)
Primary natural attacks are simply ones you use your full BAB and strength bonus on. This include things like claws (on either hand), bites, stings, etc. Secondary attacks are just awkward things like hooves that, while tough enough to deal damage, are still to hard to use effectively, so they get a -5 penalty and only half strength. Technically, when you swing a sword around, all natural weapons become this awkward and thus become secondary.
Besides that one principle of mixing where all natural attacks become secondary, you can generally think of natural attacks and manufactured attacks as in separate worlds. They have their own separate rules, and even when mixed they do not really interact that much.
Unless you mean the question of "which hand is my off hand?". In that case, I differ back the the "your left hand is not some shriveled, t-rex arm" statement. If you are not TWFing, then it doesn't matter which hand you use. I am unsure, and highly doubt, that mainhand is set as either your left or right either (although when that would come up is beyond me too)
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In short, there is no such thing as a "primary hand" , Unless you are referring to The difference between Main hand and off hand, in which case there would be no such thing as a "primary attack"
Main hand and offhand attacks have nothing to do with Primary and secondary attacks. They are two completely separate systems.
So my character has a primary attack and I am looking at a feat that says 'primary hand', would I not qualify for that feat?
I am unaware of any feat that references a primary hand, what feat were you thinking of, the term "Primary hand" is not a game term
I assume you are referring to Multiweapon Fighting again? Natural Attacks have nothing to do with that. All the references to "hands" only apply if you are using multiple manufactured weapons; if you had three arms each with a sword and wanted to get an extra attacks because of it, you could but would take heavy negatives. Multiweapon Fighting just reduces those negatives. That is all it does.
10 gp says it's this one:
Two-Weapon Feint (Combat)
You use one weapon to distract your enemy while slipping another past his defenses.Prerequisites: Dex 15, Int 13, Combat Expertise, Two-Weapon Fighting.
Benefit: While using Two-Weapon Fighting to make melee attacks, you can forgo your first primary-hand melee attack to make a Bluff check to feint an opponent.
In which case the answer is: A natural weapon may not be used as the forgone attack, because if you are exclusively using natural weapons you are not TWFing, and if you are not exclusively using natural weapons, they are secondary attacks, and in no way could be considered the "primary-hand melee attack".
I stand corrected, For some reason I was thinking the correct term was Main hand, oh well live and learn.
What do you mean by "primary attack", Mapleswitch?
Mapleswitch appears to have abandoned this thread for reasons I won't speculate on.
However, this is a good question to answer for posterity, since it does seem to crop up a fair bit.
So, example (and ridiculously hypothetical) character for the scenario: BAB +6, bite, slam, longsword and short sword, TWF feat and Two-Weapon Feint feat. I will ignore all penalties and bonuses except iteratives and secondary natural attacks.
This character has an almost insane number of possible attack combinations, but they all boil down to three selections (for simplicity, I will assume that the Shortsword is the off-hand attack whenever TWFing):
1) Natural attacks only. (Bite +6 and Slam +6)
2) Manufactured weapon attacks only. (Longsword +6/+1 and Shortsword +6)
3) Both together. (Longsword +6/+1 and Shortsword +6 and Bite +1 and Slam +1)
To use Two-Weapon Feint, the first selection doesn't work. The feat only works when TWFing, and natural attacks do not allow TWFing.
That leaves 2 and 3.
Since in selection 2, natural attacks do not enter into it, the question of whether a natural attack can be used with Two-Weapon feint is irrelevant. Which makes this really simple, since we only need to consider selection 3.
The rules for using natural attacks in conjunction with manufactured weapons are clear:
Creatures with natural attacks and attacks made with weapons can use both as part of a full attack action (although often a creature must forgo one natural attack for each weapon clutched in that limb, be it a claw, tentacle, or slam). Such creatures attack with their weapons normally but treat all of their natural attacks as secondary attacks during that attack, regardless of the attack's original type.
Now we can answer the question presented with a specific example: can this character use its bite attack as the "first primary hand attack" in Two-weapon Feint?
Answer: no. The first primary hand attack in this example is the +6 attack with the longsword (because we have designated the Shortsword to always be the off-hand) and can never be the natural attacks.
To generalise: when an ability refers to "primary hand" with respect to Two-Weapon Fighting, natural attacks can never fulfil that role.