What is the best method for clearing invoices in R12 Accounts Payables?

We have a need to create a payment template to clear invoices and credit that net to zero.  We want to use the Payment Method called ‘Clearing’.  To date, we have created a template and used the Payment Method of ‘Check’.  The system successfully marked the invoices and credits as paid; however, when we change the Payment Method to ‘Clearing’, the payment process will not complete. 

If we use ‘Check’, our monthly AP metrics for tracking the number of checks vs. electronic payments will not be accurate.  And we need to clear them off our Accounts Payable Trial Balance as a ‘Clearing’ and not waste our Check document numbers. We should have our AP Trial Balance reflecting the items remaining to pay – for our External Audits.