"but his employer want to pay only on ss# noot on EIN."

There is no Employer when your client is filing Sched C and being given a 1099 for the year. The relationship of Employer and Employee would be done with the SS and with a W2. Your client hands a new W9 to that "customer" who pays him/her and points out that either pay using the SSN as W2 employee per the labor regulations, or pay using the EIN and use 1099 for reporting to the independent contractor per regulations.

Let's clarify this: "I entered everything on his company EIN so i dont have to enter again on sch c under his ss# and put it again as a negative no."

All the business income is entered on the Sched C for that business activity; there is an EIN for that business entity, but that is not the tax paying individual. The 1099 does not control this. You would report all business income, even if no customer falls into the 1099 reporting limits.

The Sched C is a part of the 1040 for the individual, which has the SSN. That's how they relate: 1040 for the Person who is running a business, and the Sched C is for their business.

There is no double entry or negative entry anywhere.