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.
