Understand that unlike a sole proprietorship or single member LLC which is considered a disregarded entity for tax purposes, an S-Corp is considered it's own separately taxable entity. *YOU* do not pay taxes for the S-Corp. The S-Corp pays it's own taxes. You may be the one physically paying them. But you are not paying those taxes for you. You are paying them "on behalf" of the S-Corp. So you must use the EIN, and/or the separately state issued tax identification number if your state issues a separate number applicable to state taxes only.
If you use the SSN of any owner of the S_Corp, then that owner has paid any quarterly taxes that may be due, and the S-Corp has not.
