I accidentally paid my nanny taxes using form 941 and then requested that the IRS transfer my tax payments to my personal account. How do I avoid double paying?

You can indicate payments made by following these steps.

In order to indicate the taxes you have paid already during the year for your household employee (or others), you need to:

1. Go to "Deductions + Credits" (on the top bar)

2. Select "Estimates and Other Taxes Paid"

3. Select "Estimates"

4. Under "Estimated Tax Payments", select the first option "Federal estimated taxes for 2017 (Form 1040ES)"

And there you can enter the payments you have made during the year (each quarter).  

I followed this advice, and I got a notice from the IRS saying I incorrectly entered estimated tax payments.  Because Quickbooks Online asked me to get an EIN for the "business" of the household, I did that.  But then I got this Notice.  So when I called the IRS and spoke with the Tax Law Department, they told me that I should NOT have filed the 941 and 940, that the taxes are being applied to the "business" EIN.  They said that I need to request that the IRS apply the taxes paid to my SSN, and I now have to file a 941-X for each quarter that I had the nanny as well as file a 940 Amended for the year.  I am very unhappy with Intuit, which was supposed to handle all of this properly and did not guide me correctly.  I'm having to take a day off work to fix this problem.

THE ABOVE ADVICE IS NOT CORRECT. I also had the same thing happen. TurboTax is not clear with regard to this portion of the tax code. Took multiple visits to IRS to have them correct the issue.

Make estimated payments via ES-1040 (estimated payments quarterly) and use Schedule H. Do not forget to file another 941X to tell the feds your 'business' is no longer paying into the 'Employer' system.