I know this post was from a long time ago, but thought I would post an answer for other users that are looking for a solution.
I like what Rochelley posted, which is 100% correct. But, I tend to cheat a little bit to make things easier which ends with the same result, but might not be what you'd like to do. All depends.
I agree with Rochelley, create a deduction payroll item called something like Employee Receivables, and link it to an other current asset account on your COA called something similar, Employee Receivables or whatever you deem appropriate. When this is all done, this will be the only account you will have to deal with when attempting to collect the amount from your ex-employee. If and when the ex-employee makes a payment, you will Credit this account and debit your bank account.
Next, I would just go back to the paycheque where you originally paid out the commission. Take note of the net amount paid. Then reduce the commission amount to the amount he should have received. (If it was $5000 and should be reduced to $0, enter $0). Then the taxes, CPP, EI, vacation accrued, WCB etc. should all calculate to the correct amounts. (I say SHOULD because there are instances where you have to calculate the amounts manually. If you manually adjusted any of these amounts on the original paycheque, then those manually entered amounts would remain the same...and would need to be adjusted manually again to the new correct amounts. Or, if the employee has maxed out their CPP, EI, WCB for the year on that paycheque, then you may have to manually adjust the amounts in that situation as well.)
Next, in order to bring the paycheque back up to the amount that actually came out of your bank account, go to the "Other Payroll Items" and use your new Employee Receivable payroll item and enter in the difference in what the net pay shows now, and what it was originally. Quickbooks will try and turn the amount into a negative amount, but a warning message comes up and select "yes" you want to make a POSITIVE deduction on the paycheque. The paycheque amount should now equal the same amount as the original paycheque.
Now, to ensure this change is captured in your next remittance, you may have to re-run a PD7A report for just that original pay period, and adjust your next remittance accordingly so it captures any amounts that have changed.
To invoice the employee for the amount owed, go to your Item List and create an "Other Charge" type item that is linked to that Employee Receivables account. Then create an invoice for that employee using that new item. But as Rochelley suggested, you could also just do a journal entry when they pay you, to debit the bank account and credit the Employee Receivables account and skip the invoice altogether. However, I do like the fact that you can email out the invoice to the employee, along with monthly statements showing how much they owe, and you are more likely to get what you are owed. Good luck.
