Yes, you will need to fill out 2 different Schedule Cs. One for your sole proprietorship and one for the unrelated self-employment income. You should have a Schedule C for each line of work/business you have.
You should be using your EIN only for income related to that line of work/business. Any income that is not related to the sole proprietorship with the EIN should be associated with your SSN. So, the W-9 you gave as an independent contractor for services unrelated to your business should have your SSN. As long as you keep good records, you will be able to explain it in the unlikely event you are asked about it. But you should give them an updated W-9 with your SSN if that income is unrelated to your sole proprietorship.
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