You can do a couple of things:
1. Void or delete the payments, since they must have cleared your bank account prior to when you entered your opening balance/began reconciling your account. When you do this, old payroll liabilities may show as due again in the payroll center. However, they will 'drop off' after awhile if you do nothing. Or, you can enter liability adjustments to negate the balances and then they'll go away.
2. Add a deposit to the bank account for the total amount of the checks and use the Opening Balance Equity account as the account. Then perform a special reconcile and mark off just the checks and the deposit for a net 0.00 amount.