The IRS requires a single member LLC that has employees to have two Federal ID numbers(EIN). One EIN is assigned to the individual owner (as a sole proprietor) and one is assigned to the LLC. You cannot use the online application to apply for these two EIN numbers. To apply, call the IRS Business and Specialty Tax line at 800-829-4933 and an IRS representative will take the information from you and assign you the required two EIN’s.
For payroll purposes only the EIN assigned to the LLC is used. The EIN assigned to the sole proprietorship is used only in preparing your personal income tax form. The IRS links, internally, both of these numbers together. When the State requests an EIN number, in registering, submit the LLC EIN.