If you still have a payroll to do for December, you can manually adjust the CPP deduction to what you need it to be.  Then you just remit it to CRA the same way you have done with your other batches.  Of course this is going to reduce the employee's pay as well. 

CPP deduction never took place since March, so it is over 1500 dollars and I do not want to deduct all from employee's pay cheque and leave her with nothing close to Christmas.

If I record the same amount into regular and same into CPP deduction, then wouldn't that increase the employee's income for this year.

what are the ways to balance it for this year and pay both portions out and recover it from employee over the next year.

The problem with not entering it on the employees payroll and you submit their T4 to the government at the end of the year, it will flag the CPP for that employee and they will be calling you.  You can pay it to the CRA but then without the other side done, that will flag as well that you overpaid taxes etc. compared to the t4's. 

Nazish:

If you want to look after the CPP before the calendar is over you can calculate what the employee CPP is owing and include it on a manual paycheque but code the balance owing as an advance for the employee. As the employee repays from pay period to pay period code it to the advance. If you do this turn off the vacation pay for the manual cheque (zero amount).

That was helpful. so what i did was to put the amount into loans and the same amount under CPP and made all other deductions are zero. doing that the pay cheque was zero and allowed to do remittance. i did not process it as advances because now the advances are taxable.  Now I believe all i need to do is collect that amount from employee over the next year.