The IRS considers a single-member LLC to be a disregarded entity. So it doesn't matter if you pay estimated taxes under your SSN, or your EIN. The EIN is tied to your SSN, so it doesn't matter.
Also, the way you worded your question makes me think you are "paying yourself" as an employee of your LLC. The owner of a single-member LLC is not, and can not be, an employee of the business. Under no circumstances will you ever issue yourself a W-2, 1099-MSIC or any other type of tax reporting document. Income earned by the business is considered income earned by you. The only difference is, you will pay an additional 15% (approximately) on the income earned by the business. That's the Self-Employment tax, which is basically the employer side of Medicare and Social Security.
Do note that if you are on QB 2017 or older, I don't know if you'll need to update to the 2018 version for the new tax laws.
@johnbaxtertrabol No, the owner of a Sole Proprietor does not owe Federal Unemployment tax on their business profit. I am not aware of any States that require it either, but you may want to check with your State.
In the event the Single Member LLC has filed the election to be taxed as a corporation, that changes things, and I would HIGHLY recommend going to a tax professional if that is the case.
Pigy-backing off of this question. I am a single-member LLC and I have an EIN. I enrolled in EFTPS to pay quarterly taxes under that EIN. My accountant told me to pay under form 1040-ES, but that form wasnt on the list. After talking to a customer service rep at EFTPS, they said that 1040-ES will only show up if you are registered under your SSN and that I must use 941 to pay under the EIN. Is this going to affect anything, or will everything be fine if I pay under 941, as a single-member LLC?
If your single member LLC does not have any employees then your accountant is correct. Note that the owner of a single member LLC can not be an employee of the business they own.
So if you have no employees you can pay at www.irs.gov/payments each quarter, and do so under the SSN of the business owner. Otherwise, with employees you must go the 941 route. Now for the 941 depending on the income of your business, you "could" be required to file the 941 monthly. But for 90% of small businesses with employees, they don't come anywhere near that requirement and are just fine filing/paying quarterly.
Note that if your state taxes personal income, the filing requirements for state taxes could be different from federal taxes. So don't let that get past you or the fines and penalties will be a real killer at tax filing time.
When paying your quartarly estimated taxes are you required by the IRS to send in the exact same amount every quarter?
Or can you just calculate what you make each quarter and send in 20% of that?