After you file

I assume you are a sole-owner of the LLC, in which case you were correct to use the TurboTax home and business software to prepare a schedule C reporting the business income and expenses. I think you mean with the estimated payments that you reported them using the federal identification number of the business as opposed to your personal social security number. If so, you will need to file a partnership tax return for Wisconsin to receive the estimated payments back. That would be Wisconsin Form 3. You can fill it in online, here is a link:  Wisconsin Partnership Return Enter $0 for the tax on line one and your tax withheld on line 5. Your refund of taxes paid in will appear on line 12.

For your state personal return, go back into TurboTax and remove the state estimated payments you entered and pay in the state tax due. You will get a refund of the taxes you paid in under the LLC ID number.