Hi phburke,

You can record the past due payments as prior payments in QuickBooks. Then, choose Do not affect accounts to avoid duplicate posting on your accounts.

Please check out this article for the detailed steps: Enter historical tax payments in QuickBooks Desktop Payroll.

QuickBooks used the default Payroll Liability and Payroll Expense accounts. You can change the correct expense account by going to Lists, and the Payroll Item List. Just edit the item to correct it. 

I'll be here if you have any payroll questions.