If an S corporation receives Form 1099-K, Payment Card and Third Party Network Transactions, most likely the amount in Box 1 is already part of the gross receipts in their books and doesn't need to be entered separately.
Verify with the company bookkeeper that the amount on any 1099-K is part of the gross receipts they reported to you. If it's not part of their gross receipts, you'll need to include the amount in Box 1 in Gross Receipts in the return, and they will need to double-check their bookkeeping to determine why it's not part of the gross receipts in their books.
In the tax return, to make it clear what's going on, you may find it useful to itemize the gross receipts in the return to clarify the portion reported on Form 1099-K and the portion from other sources. This information will print as a supporting statement with the return. To do this, at the "Gross Receipts or Sales" field, press the F10 key on your keyboard, to arrive at the window headed "Statement for Gross Receipts or Sales". Select New, enter the description, then the amount. Your entries in this window will summarize and carry back to the gross receipts income line.