See here to start.
https://www.irs.gov/faqs/small-business-self-employed-other-business/forms-940-941-and-944-employmen...
And really, it would be worth it to get an accountant to help you the first year, so you get your books and procedures set up properly. I don't know about forms 940, 941 and 944, but the penalty for filing the S-corp return late (was due March 15 and no COVID extension) is $195 per month.
Generally, you must file form 941 quarterly to report and pay the employment taxes due that quarter. You pay the taxes with the form. You can file the reports late, but since your payments will also be late, you may be assessed interest or a penalty. I'll come back to that.
You file form 944 annually instead of 941 quarterly, but only if you have a "small payroll" and if you are approved in advance to file form 944 instead of quarterly 941s. If you file quarterly 941s, you don't also file a 944.
For the end of the year, you file a form 940 to pay federal unemployment tax (FUTA). If you are not subject to FUTA as the single shareholder of a small business, you would not file this form at all. I can't help you here, the only forms 941 I filed were as treasurer of a church, the only employee was the pastor, and the church was exempt from FUTA so I never filed a form 940.)
Also for the end of the year, you prepare a W-2 for each employee, filed with the social security administration. Form W-3 is a summary that totalizes all the income and withholdings across your employees (which is 1 in your case so the numbers should be the same as the W-2.) If you use an electronic service to prepare your W-2s such as Quickbooks, it should automatically prepare the W-3 as well.
Don't forget that you may be required to file a similar form or forms in your state, to report state employee withholding and other things.
**Don't pay any penalties now, wait until they are assessed by the IRS. You can then apply for a penalty abatement (forgiveness) if it is the first time you owed a penalty. Interest owed on late payments can't be abated or reduced, although abating the penalty will reduce the balance on which the interest is computed.
