Are the 1099s show more than what the actual income was?

I don't understand your second question. You enter the amount of income that the corporation received.  Can you clarify what you mean?

The 1099K shows more than what the deposits in the bank are. The reason is because the 1099K shows the credit card charges that the customer pays.. Ebay withholds funds from the seller for various fees and deposits into the seller's bank account the customer charges minus fees. The deposit into the bank is much less because of the fees withheld. If the IRS matches the 1099K to the S corp income, the income is much lower than the 1099K. Does the IRS match for S corps or only for Sch C filer? And should Gross Receipts on the 1120S be the same as the 1099K ( meaning I gross up the deposits) or can Gross Receipts equal bank deposits ( customer sales-fees)? 

Yes. No. Yes.

Gross Income is income before any expenses, which would include fees charged by whoever. Generally speaking Gross Income is more than that reported on 1099s, because most businesses receive income from sources that are not reported on 1099, e.g. cash or check from personal or business accounts. 

What IRS matching might have done last year is different from what it might do this year, and then next year it might go back to the old ways. Predictions are difficult, especially when they involve the future.  It's also possible that IRS will run a pilot program involving only 5% of 1099's issued to certain categories of taxpayers. 

The gross sales, before fees, should be reported as income.  Then the fees should be deducted. 

"The reason is because the 1099K shows the credit card charges that the customer pays."

Let's restate this.

The Seller has to collect the full amount. Their processor will hold back fees, commissions, etc, and forward the Net.

You are confusing Banking and Sales.

Your client "got" the full amount. Then, their processor, when that applies, took care of their next step in sorting out the destination of various parts of the total paid. Your client does the same thing internally, if there is (as an example) a cash sale.

"deposit into the bank is much less because of the fees withheld"

The business financial records should show these fees as Expense. How do you manage a business and shop around for a better processing agent, if you don't track what you pay in fees already? How does the IRS know you have any business expenses if all you report is Net income?

You do not report only the outcome. You track and report everything. Just because it isn't in their hands when that step was done, doesn't mean they did not incur it. It was processed on their behalf and those are their fees.

Thank you all!