AS bids your entire amount once in the final seconds, just as if it were you sitting at your computer. If you are familiar with eBay's proxy bidding system, you know that in the winning bid is generally in the amount of the second highest bidder's bid plus one increment. So if the second highest bid is for $507 and you bid $1000, you would win for $517, which is the second highest bid of $507 plus the next increment, which is $10 at that range.
You may sit at your computer and also bid manually during the closing seconds, if you like; this will not interfere in any way with AS' activity. However, just know that if you win the auction, even by your own manual bidding, AS will still deduct its fee--unless you are still using your original three free snipes!
Good luck and let us kinow how it turns out.