USA 1120S vs Schedule C

[smallbus2011]

I filed a 2017 1120S without a salary and elected to make a late election under rec-proc 2013-30. It was denied because of the late filing of the return however I have documentation that it was timely filed, so I think I could maybe get around that. The net was so low that it isn't really beneficial at this point to file as an 1120S since I would have to pay in payroll taxes (late file/late pay/interest etc.) My question is - Do I file an amended 1040 and just add the business income to the Sch C? If so, what do I do about the 1120S that was filed - just leave it out there since it was not accepted anyways?