I have been writing payroll checks to myself, and deducting taxes from gross wages and paying taxes monthly and reporting Quarterly Reports.
I gave myself a W2 and filed a W3. All of this income went to me the owner.
Do I reduce my General Income by these wages, where/how do I expense my pay?
Yes to the previous answer...but in addition, you don't report your W-2 income on Schedule C, you report it as W-2 income.
In fact, you don't even report a Schedule C at all.
There are some self-employment benefits that flow from the 1120S to you through the K-1, but there is no Schedule C involved (think: self-employed health insurance deduction).
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Just to be clear, did the corporation file a SEPARATE tax return that was due last March? That is what needed to be done (and I REALLY recommend going to a tax professional for the corporate return).
Let's start from the beginning here.
First, there is no such thing as a "sole proprietor LLC S-Corp". You've combined three distincty different types of business.
A "sole prorietorship" is one type of business. The IRS considers this business type to be a disregarded entity that reports all business income/expenses on SCH C as a physical part of your personal 1040 tax return.
A "single member LLC" is a Limited Liability Company with only one owner. The IRS also considers this business type to be a disregarded entity that reports business income/expenses on SCH C as a physical part of your personal 1040 tax return.
An "S-Corp" is yet another type of business. The IRS considers this type of business to be a separately taxable entity. An S-Corp is required to file it's own physically separate tax return on IRS Form 1120-S. That form has to be signed by an officer of the S-Corp. With you being the only owner, that would be you.
The S-Corp will then issue each owner a K-1, which each owner will require in order to complete their own individual 1040 tax return.
The owner of an S-Corp is "REQUIRED" to take a minimum distribution from the profits of the S-Corp every year. Additionally, the owner of an S-Corp can also be an employee of that S-Corp that the S-Corp will issue a W-2 to. You would then report that W-2 on your personal tax return just like you would any other W-2.
Now lets get in to where it appears you really mesed up here.
While the filing deadline for the personal 1040 tax return was extended to July 15, 2020, the filing deadline for your 1120-S corporate return was March 15, 2020 and it was "NOT" extended. So as it stands now, you are 4 months late in filing the 1120-S corporate return. The late filing penalty for that is $200 per month, per owner. So with you as the only owner your late filing penalty is $800 at this point in time as of the date of this post.
You can't even start your personal tax return until you have completed the corporate return and the corporation has issued you your K-1 (in addition to your W-2 if applicable). On top of that, it's now to late to file for an extension of your personal return.
Bottom line? Get professional help yesterday, if not sooner. You don't have time to play around and "learn" at this point. You just need to "get 'er done" and keep your fines and penalties from increasing.