Hmm, I feel like we need to go over what counts as taken out first.
A character is taken out of a conflict, when they have to take stress that they can not fit on their stress track and can't or won't absorb any other way.
So for example, we've got your vampire with a stress track of OOO (OO), which means he's got inhuman toughness. Now let's look at a few scenarios.
1) You attack him with a fists roll of +6, he only rolls a +3 on his athletics, even taking into account any speed powers. Say you're a werewolf with inhuman strength and claws, that means you inflict 3+2+2=7 shifts of stress. That gets reduces to 6 shifts because he has armor:1 from inhuman toughness. His stress track is only 5 boxes long, so if he doesn't do anything, he's taken out.
1a) One option would be to spend a fate point to increase his defense roll by +2. That would bring the attack down to 4 shifts and he would mark his stress track like so: OOO (XO). He would not be taken out.
1b) He could also take a consequence. If he does, the attack gets reduced by a number of shifts depending on the consequence he takes. A mild consequence is worth 2 shifts, a moderate 4 and a severe 6 shifts. So he could take a mild consequence and call it "scratched up" and get the same result as above. A moderate consequence is worse than a mild, and it could be "severed feet", which would lead to a stress track like: OXO (OO) + moderate ("severed feet"). Usually, severed feet would probably be a severe consequence, but on a vampire, it's probably less severe.
You can find the description of what the consequences should roughly be in the book.
2) Now lets look at the same attack with the werewolf being doused in holy water before, so he satisfies the catch. He can't use the stress boxes in brackets anymore, and his armor goes away as well. That means we are dealing with a 7 shift hit on a OOO stress track.
2a) A fate point won't be enough now. He'll need to spend a fate point plus a mild consequence to stay in the game.
2b) Or alternately, he could take at least a moderate consequence as above and stay in the game. But again, a mild alone won't cut it.
3) Filled stress boxes. Now in the course of the fight, the vampire has already taken a few hits. His stress track looks like this: XOX (XX), and he has to take a 3 shift hit. Now 3 shifts isn't all that much, but his 3rd stress box is full, so it rolls up to the next free stress box. In this case, there is no free stress box larger than 3, so this hit would take him out. If he still has consequences left he could reduce the attack to a 1 shift attack, which would roll up to the 2nd stress box, but he would stay in the conflict a while longer.
Only if a character can no longer soak up all the stress he takes, whichever way he does is irrelevant, he is taken out of the fight. So it can happen that a character has a full stress track and the next 1 shift hit takes them out. But it can also be that they take an 8 shift hit and still stand.
So the amount of stress in one attack doesn't automatically have anything to do with taking out a character. But if you inflict that final blow, you are allowed to say what happens with the character that has been taken out, as long as it is withing reason. So kicking someone and turning him into a pile of money is probably not possible. Kicking their head off? Might be a bit over the top but this is basically a fancy way of declaring him dead, so it's all good. You've got full control over what happens with the taken out character. Other players can make suggestions, of course, but you can decide what happens.
Also, keep in mind that consequences are named by the party that takes them, not the party that inflicts them. So while "severed feet" might be a good consequence, the player (or GM, if the vampire is an NPC) might choose to name the consequence differently. Though you can still make a suggestion, of course, but the final judgment is with the player who takes the consequence.
Other question: if character is NPC can I ignore the skill progression (1 Skill 5, 2 Skills 4 etc)?
It's not so much a progression as it is just sorted in columns. Generally though, I don't bother with the columns on most NPCs. I just decide how good they are in some key skills and the rest defaults to +0. Or another value, if I decide they are better than that. Could be that they get multiple +5 skills and no other skills as well. I just build them how I see fit. The skill columns are mainly there to balance PCs.