The IRS will definitely be looking to match the 1099-K amount; that's the whole purpose behind filing those forms so the government can match both sides of the equation.
Having said that, this is only one part of the puzzle; the gross amount. This gross amount will be reported on line 1 of your 1120S. You will then report all your expenses on the applicable lines 7-19. This will then provide you with your appropriate net income. This should also provide you with the same result as if you were using your bank records.
*A reminder that posts in a forum such as this do not constitute tax advice.
Also keep in mind the date of replies, as tax law changes.
