Here is the Error to correct: "Previously, we just knew to send the check and we added it as a bill then paid it"

It was never a Bill. You would have used Create Custom Liability Payments.

Now you need to look at what you put on the Bill; did you post it as Expense or as Liability? As Expense = never employer expense. As Liability = you broke the relationship between Payroll item and Payroll Liability account tracking.

Here's how to fix it. For each Bill you made, you will use Pay Liabilities now, selecting the overdue payment and this Pay Liability Check will be for the same date and check and amount as you paid using the AP method. Click on the Expenses tab of this Pay Liability check and put here the same account you used on the Bill that was the error, but using negative Amount. Now hit the Recalculate Icon. This is a $0 Payment, it paid the liability the Right way, and it offsets the bills that were done in error.

If you paid it out on Bills as expense, this will change your Financial reporting, because they were Wrong all along.

if you paid it out on Bills as PR Liability, this doesn't change the Financial report.

Both conditions, you Fixed Payroll by using Pay Liabilities, now, and making them so that they offset the earlier mistakes.