The customer is not required to issue a 1099-NEC if you are taxed as an S-corp. You would document that by giving them a form W-9. If they insist on issuing a 1099-NEC, try to make sure they use the corporations's tax number. The income would then be reported as company income on your 1120-S. There is no need to "pass it through" a sole proprietorship in your name on schedule C.
