Oh dear. I think you need to get to an accountant to educate you and help you set things up, at least until you are able to do this on your own.
A single member LLC is a "disregarded entity." This means it is reported on a schedule C attached to the taxpayer's tax return. The schedule C lists the business gross income and expenses, and calculates the net profit. The net profit flows as income to the main form 1040, where it is combined with other income, spouse's income, personal deductions and dependents, to calculate the income tax due. The business income also flows to schedule SE to calculate self-employment tax, and the total income tax plus SE tax is what you owe the IRS.
A disregarded entity never issues a W-2 to the owner. If he issued a W-2 including filing form 941, 944 and W-3, all that needs to be reversed and corrected.
A single member LLC may choose to be treated as an S-corporation for tax purposes. In this case it could probably issue a W-2. The LLC would be required to file a separate corporate tax return, this is due March 15 (not April 15), the deadline is not extended due to COVID, and the penalty for late filing is $195 per month per owner or member. The corporate return issues a K-1 form to the member, which is included on the member's personal tax return. See this for more.
https://www.irs.gov/businesses/small-businesses-self-employed/limited-liability-company-llc
A multi-member LLC must file a separate corporate return by March 15, unless there are only two members, they are spouses, and live in a community property state--in which case the LLC is treated as 2 separate disregarded entities. An LLC with more than one member who are not spouses must file a corporate return.
