It depends entirely on your bookkeeping system. If you know for certain that the income reported to you on a 1099-MISC is the same as the income from reporting one or more of your invoices, you would not enter the 1099-MISC as it would be duplicating your revenue. It makes no difference which one you use for your tax returns.
Ir would be best if you could actually match the 1099s to specific invoices and note that information in your own bookkeeping system. You always want to make sure your internal income is reporting at least as much as the 1099 totals. You also want to be sure that the 1099s sent you to you accurately reflect your income for that job. Customers do make mistakes.
