You clients can report using either your SSN or your EIN. Each should use the TIN shown on the latest Form W-9 that you gave each. Having a mix is not an issue since you must report all of the income on Schedule C either way.
When in doubt, refer to the IRS instructions for a particular form. Schedule C is part of your individual tax return, so it must always have your SSN. Since you now have an EIN for this business, the EIN is to be included on Schedule C line D.
A sole proprietor pays self-employment tax by it being included on Schedule 2 line 4, calculated on Schedule SE. It becomes part of your overall tax liability, so you need to factor that in quarterly when making quarterly estimated tax payments.
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