That depends on how you've been paying yourself.
When you "work" for an S-Corp, you are an employee and the S-Corp should be paying you a wage appropriate for the work you do. This means that the corporation pays the employer portion (1/2) of your Social Security and Medicare when processing the payroll, you get a W-2 for the wages you are paid and when the S-Corp files it's tax return, you are issued a K-1 with your owner's share of the net income reported to the IRS.
If you have not been paying yourself a wage from the S-Corp either in 2015 or in prior years, then you don't necessarily have to file prior year S-Corp returns and amend your personal returns. That's because when you file a Schedule C, you, the individual, pays all of the self-employment tax that is due on the net income. You should not, however, use your EIN from your S-Corp when filing a Schedule C with your personal return.
If you have been paying yourself as an employee and withholding taxes as appropriate, you may be paying more Social Security and Medicare Tax than you should by completing a Schedule C depending on how you have been reporting things.
So basically, it's okay to file as a Schedule C with your personal return but you should not use your S-Corp EIN on the Schedule C or have payments issued to you with that number.
