1099's will only be issued to vendors who have the 1099 option enabled and who received payments last year for accounts mapped to 1099 boxes. So, having additional vendors on your vendor list won't hurt anything.
1099's won't be issued to Customers because customers are not contractors and don't receive compensation from you. If you do have an individual on your customer list who also works for you, set them up as a vendor and pay them as a vendor. In your case, after creating the vendor, edit the checks you paid to the customer version of the name, pick the vendor name, and then save the check. Then the 1099 feature will be able to 'see' the payments.
