If the 1099-MISC's were issued for work done in/by your SCH C business, it doesn't matter if it has your business EIN or SSN on the 1099. You can enter them all for the SCH C.
When you applied for an EIN you had to provide your SSN to the IRS so the IRS will know what SSN that EIN is tied to. Since they know, it's not an issue.
In the future, I would recommend that you never, under any circumstances provide your SSN to any of your business clients. That's why you got an EIN for the business.
If someone abuses your SSN, they can destroy your entire life.
If someone absues your EIN, then that only affects the business.
Never provide your SSN to a client under any circumstances, and with no exceptions. They get your EIN only, or they can go elsewhere.
