Dear Bridha ji, Firstly, your question is not clear. Is your organization covered under the Factories Act? Since you are referring to the "Manufacturing Process," if your organization is a manufacturing unit, the contract works and workmen are also covered under that category.
For the purpose of ESI coverage, manufacturing is not a criterion. Once the principal employer covers, the contractor is also covered. Since you are paying through your sub-code, there is no problem.
You have to maintain all the registers and records as per the "Contract Labour Act," not the Factories Act. Any registers required should be maintained by the Principal Employer.
Regards, PBS KUMAR