Yes, I understood what you had asked. And yes, you would still pay AS, because they still sent the bid and did the work. You do not pay them when you bid and lose the auction, but you do pay them when you bid and win, even if a previous bid by you, placed manually, won the auction for you. Considering that you are not charged at all for a lost auction, I would say that the mere pocket change you would pay in the situation you described is well worth the advantage, wouldn't you?
The point of AS is to NOT bid manually early on, but to bid solely at the lasst minute through AS. And NEVER bid an amount that you are not willing to pay!