How does the company pay social security for its employees?

Are you talking about employees buying social security themselves? If there is, fill it all in the salary slip, and then the social security bureau will check and say that he paid it himself. Also, you said that the company paid him social security in full, and the part he didn't pay himself could be deducted from his total salary.

Further reading: How to buy insurance, which is good, and teach you how to avoid these "pits" of insurance.