As a single member LLC you do not pay yourself a wage and issue a W-2. Since a SMLLC is a disregarded entity, the business and the owner are one and the same. As such, you cannot be an employee of yourself.
Your earnings are the profit that is reflected on your Schedule C and you then pay self-employment tax on this bottom line when you file your tax return.
You are going to have some issues here to get this resolved. You should file amended payroll forms requesting back all payroll amounts sent in. Issue an amended W-2 with no wages and no withholding. The reason you need to do this is because you cannot technically deduct the wages you paid yourself. As a result, you will be paying self-employment tax on your net profit (without any deduction for your wages) and you will have paid in FICA tax on your wages; essentially paying FICA twice on your wage amount.
If you are comfortable handling the above on your own, go for it, however, I highly recommend you consult with a tax professional who can handle this for you.
*A reminder that posts in a forum such as this do not constitute tax advice.
Also keep in mind the date of replies, as tax law changes.
