When paying estimated taxes, how do I connect my SSN and my EIN?

I started a consulting business (sole proprietorship) and obtained a taxpayer identification number from the IRS so that I would not have to divulge my personal SSN when transacting business. I have given clients the EIN and they have reported payments using that number. Now it is time to pay quarterly self-employment taxes and I don't know whether to pay the taxes under my own SSN or under the EIN I created. If I use my own SSN to pay the self-employment taxes, then how will the IRS connect my SSN with the EIN which has had payments reported to it? I still do not want to give my personal SSN to clients because this opens the door to identity theft.