Doesn't matter which one. Your choice.
how it'd work is all your natural attacks would be secondary, and your flurry attacks would be primary. doesnt matter what order you make them in, if you're doing them all in a round, that's how combining them works. period
Secondary Natural Attacks normally come after manufactured weapon attacks, but there is no rule one how attacks play out. If you really wanted to, you could as at BAB 16, take your -15 attack first, and go up ascending order.
The only thing FCT does is let you use a natural weapon instead of an unarmed strike for the FOB.
If you do Unarmed Strike (Normal) Unarmed Strike (FOB) then your natural weapons, are all secondary weapons and take the -5, along with only getting 0.5x str to damage with Natural Attack rules.
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There is a rule about BAB attack order. You have to attack with your highest BAB attack first then go in descending order. It gets confusing when there are extra attacks, but for a BAB +11, you have to go +11/+6/+1.
You never get to take natural attacks in addition to flurry of blows. Feral Combat Training lets you take your fliurry attacks with a natural attack. If you have three flurry attacks and FCT (bite), you could make three bite attacks, not three unarmed strikes and a bite.
I’m on my phone, so quoting is difficult. I’ll post citations later tonight.
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Following up.
If you get multiple attacks because your base attack bonus is high enough, you must make the attacks in order from highest bonus to lowest. If you are using two weapons, you can strike with either weapon first. If you are using a double weapon, you can strike with either part of the weapon first.
BAB attacks go in descending order. It’s unclear whether something like a haste attack would come after the full BAB attack or at the end. You just can’t elect to take your -10 Attack first because, for example, you know the enemy has an AC bonus against the first attack in the round.
Natural attacks in flurry... Hmm, Unchained Flurry is less specific about this than Core Monk flurry.
A monk with natural weapons cannot use such weapons as part of a flurry of blows, nor can he make natural attacks in addition to his flurry of blows attacks.
For Unchained, Mark Seifter weighed in on it HERE
"He takes no penalty for using multiple weapons when making a flurry of blows, but he does not gain any additional attacks beyond what’s already granted by the flurry for doing so." Natural weapons are weapons, so you don't gain any additional attacks for using them.
Finally, the Feral Combat Training FAQ explains how the feat works.
Feral Combat Training: What does “with” in the Special line for this feat mean for monks making a flurry of blows?
Normally a monk who has natural attacks (such as a lizardfolk monk with claw attacks) cannot use those natural attacks as part of a flurry of blows (Core Rulebook 57). Feral Combat Training allows you to use the selected natural attack as if it were a monk weapon—you can use it as one of your flurry of blows attacks, use it to deploy special attacks that require you to use a monk weapon, apply the effects of the natural weapon (such as a poisonous bite) for each flurry of blows attack, and so on.The feat does not allow you to make your normal flurry of blows attack sequence plus one or more natural attacks with the natural weapon. In other words, if you can flurry for four attacks per round, with this feat you still only make four attacks per round... but any number of those attacks may be with the selected natural weapon.
So with dragon shaman you get 2 claws (primary) and 1 bite (primary).
I assume with FCT that I can only choose claws or bite depending on what my weapon focus feat selects but I'm wondering if its possible to do 1 bite, 2 claws, and then the extra attack from flurry at 3rd level (2 levels druid, 1 monk) if my weapon focus is claws.How would this work? Since they're both primary does it matter which one I choose?
edit: sorry this would be at Fourth level to get FCT. 1 fighter level dip.
Ok, here's the deal: If you make a Flurry of Blows, you never get attacks that you wouldn't get by using a single weapon (or unarmed strike without using the TWF rules, in case you have an ability like Medusa's Wrath). Your 4th level character has a Flurry routine of +3/+3. If you decide to make a Flurry of Blows, that's what you get, period (that's the BAB values, so adding in strength etc. You also add in abilities that specifically modify an existing full attack, like Haste). It doesn't matter if you have two weapons, armor spikes, and a bootblade, plus hoof, wings, a bite, and a gore natural attack. Two attacks, period.
If you decide to not use Flurry of Blows, you follow the normal full attack rules and natural attack rules: You can combine manufactured weapon/unarmed strike attacks with natural weapon attacks, by making the latter secondary natural weapons for that full-attack action.Let's say you have FCT and Weapon Focus with both Bite and Claws, you could make a Flurry of bite/claw, claw/bite, bite/bite, claw/claw, unarmed/bite, bite/unarmed, unarmed/claw, or claw/unarmed. In any case, two attacks. Of course, unless you have both an ability that triggers on claw attacks and an ability that triggers on bite attacks, and want to trigger both in the same round, there's literally no reason to have FCT with more than one natural weapon.
Short version, if you have multiple natural attacks, using Flurry of Blows via Feral Combat Training is a trap option.