Deduction Error in Payroll

Hi, I'm currently new on sage especially payroll. I didn't notice that I have deducting one employee for medical and insurance plan. We are planning to give it back to the employee the whole amount but there's a deduction for CPP and EI. We thought about issuing him a regular cheque, but the amount on the year to date wont be cleared. How do we clear the amount in the year to date at the same time giving it back the whole amount?