How To Pay PF Arrears Payment - Trainee To Employee?

Dear Sir, We are promoting one person from Trainee to Management employee for the month of January'17 and his appointment date with effect from Sep'16. before trainee he has not having PF number. how to create new pf number and how to made contribution from Sep'16 to Dec'16.
please clarify...

so since sept 2016 the company has not filed the EPF contributions? if yes then why his name was not included? retrospective effect under the ESIC and EPF from employer side is dangerous,
how will the employer deduct the employee's contribution from the salary which is already paid?

after login, go to payment > ECR > download ARREAR (mention month current)
this format would be helpful to make payment