Single member LLC estimated taxes

[aromaticseltzer]

I have a single member LLC which is not a corporation (ie I am treating it as a disregarded entity). Last year, I made estimated tax payments on the EFTPS website under my EIN (form 944).  I realize now I should have paid under my SSN/used form 1040 ES.

When I filed my taxes, I was instructed by the turbotax live help to put the amount of prepaid taxes on my 1040 line 26 (estimated tax payments). I got a notice from the IRS correcting this to $0 (essentially ignoring the prepaid taxes). How do I get the IRS to recognize the prepaid tax that I filed under my EIN? Is there another form I need to file? Is there somewhere else on the 1040 I need to put it to correct this?

[MaryK4]

You will probably have to file (if you have not) or amend (if you did) the 944 to get a refund of the deposits you made.

[aromaticseltzer]

Thank you for your response. Since I reported all my business income on my 1040/schedule C, and paid the self employment taxes based on my 1040, and did not pay any wages to any other individual, should I report my wages etc. on form 944 as 0? 

[ZoltanB45]

You do not need to file a 944. You are not an employer if you don't have employees. As an LLC owner, you don't give yourself salary, so those forms are not relevant. 

[aromaticseltzer]

I appreciate your response. How would you suggest I get my estimated tax payments back, if not by filing form 944?

[GeorgeM777]

Here is another option you might consider.  Because you filed Form 944, and perhaps incorrectly, you may need to file an amended Form 944 to reclaim the estimated tax payments, i.e. Form 944-X.   

The instructions for Form 944 seem to support filing an amended Form 944-X.  In this regard, the instructions state the following:

• If you need to adjust any amount reported on line 6 from a previously filed Form 944, complete and file Form 944-X. Form 944-X is an adjusted return or claim for refund and is filed separately from Form 944.

You will need to complete Form 944-X manually and mail it to the IRS.  Part IV of Form 944-X is where you can provide an explanation for your changes.  

Here is a link to Form 944-X and the Instructions to Form 944.  

Form 944-X

Form 944 Instructions

@aromaticseltzer

[aromaticseltzer]

@GeorgeM777  @MaryK4 To clarify, I have not yet filed form 944. When paying estimated taxes on EFTPS, I had to associate those with a form from a drop down menu, and chose form 944. The reason I chose that form was because of a letter I received from the IRS when I first created the LLC instructing me to file that form. 
So, since I have not yet filed a form 944, I would use 944 rather than 944 X, correct?

Also, should I provide some kind of explanation with this form indicating that the income was already accounted for on my 1040?

[DianeW777]

Do not file Form 944 because you are not required to collect or pay withholding tax.  Instead explain in a letter about your EIN and your social security number (SSN).  Let them know the payments you made need to be transferred to your SSN.  This should clarify the situation for the IRS and the payments should be transferred.  Furthermore, explain the details about your payment and that it was applied to your Form 1040 because your are a SMLLC.