If you have an S-Corp, the S-Corp files the 1120S, and you still file a Form 1040 for yourself. Your S-Corp should give you a Schedule K-1, which you will use to complete Schedule E on your Form 1040. You do not file Schedule C because, for tax purposes, you are an employee of the S-Corp rather than self-employed. (The fact that you may own all shares of the S-Corp doesn't matter.)
The deadline for S-Corps that have a calendar year as their fiscal year was March 15, so you're probably already late for 2016 on the S-Corp.
Also keep in mind that the S-Corp is obliged to pay you a wage, so there should be employment taxes involved, which may or may not balance out if you tried to pay self-employment tax via your Schedule C. The S-Corp really should have issued you (and filed with the Social Security Administration) a W-2 for you as an employee each year.
At this point you better get professional help. Probably you'll need to file (late) a form 1120S for all of the missed years, get the corresponding Schedule K-1 for your personal tax for each year, and then file amended personal returns on Form 1040X for each year.
Really, though, better get some help professional help at this point.