The amount you enter as your bid in AuctionSniper(AS) is what it bids. In your example, AS submits your $40 bid say 5 secs before the end of the auction. If the competing bidder's max bid is $25, you will hold the winning bid at $26 with your $40 bid held as proxy. With less than 5 seconds to respond, the competing bidder will probably not be able to counter bid. And even if he could, he still might not beat you -- he may counterbid $30, which means you would win with a $31 bid, with your $40 bid held in proxy.
Thats why you'll always see folks here recommending to enter your MAX bid in AS. That way, if you win -- Yay! & if you lose, you didn't overpay. They also recommend entering an odd bid, like $40.14 instead of $40. That way, if your competing bidder entered the even amount of $40, you can win by $0.14!
The ONLY thing that AS might change from what you tell it is in lead time. Since AS is continually interacting with ebay with snipes, wins, & losses, the program can detect when the ebay program is interacting slower than normal. At these times, the AS program may enter your snipe sooner than you specify to make sure the bid gets place in time.
Hope this helps.
Jabbergah