Here's what I do when an error has been made on an employee's pay cheque. First of all, make sure you have an other current asset account set up for Employee Advances, and a payroll item called Employee Advances, linked to that other asset account. Do not use the QB built-in Advance item here, as that usually posts to a wage expense account and we don't want that in this situation.
Go back to the pay cheque where the error was made. Open it and take a screenshot of it or print a paystub to refer to it.
Edit the pay cheque to the way it should have been when it was issued. Whatever the net difference is, you will put into an Employee Advance in the other payroll items section of the pay cheque; this will give you the same net amount as the first cheque you already issued, as the net amount cannot change, for obvious reasons.
On a future pay cheque, reverse the Employee Advance item in the same amount as it was on the original pay cheque. This will clear the overpayment you made to the employee, which will have been tracked as an advance in the asset account, not affecting wages at all. It's like saying, "Oops, we paid you too much so it is being treated like a short-term loan from the company, which will have to be paid back on the next pay cheque."
Now your CRA Payable will be altered. If this occurred long enough ago that it affects a prior PD7A remittance period, re-print your PD7A for the payroll period in which the error happened, and keep that as your accurate record of what the remittance should have been. Don't throw away the first one - - you still want to have a trail of what happened and why. Obviously, you have remitted too much. Figure out what the differences are for each of the Income, Federal Tax, CPP & EI in the period where you made the adjustments. Write those adjustments down on the current PD7A remittance that you have yet to make. Tally each item with the adjustment, and that is what you'll pay for this remittance.
When you use QB to pay payroll liabilities, the total amount of your current remittance will be correct, as it will have included the differences that were created when you edited the pay cheque. When I create the QB 'cheque' for the liability payment, I edit each payroll item to what the current remittance numbers should be; then I list the same payroll items again, entering the amount of the adjustment only for each of CPP-Company, CPP-Employee, EI-Company, EI-Employee and Federal Income Tax. The net amount to the CRA will match your adjusted PD7A for the current remittance. I think I may have outlined this whole procedure in another post with screenshots. If I can find it, I will send you the link. Otherwise, you could search posts by @Rochelley and you should be able to find it easily enough.
Good luck!
