@Dixon FDS 

A much easier way to handle applying A/R to A/P or vice versa is to create a bank account called 'Clearing Account'.  This is just a temporary account used to hold the offsetting amount. 

If you're applying A/P to A/R, pay the bill using the Clearing Account.  Then, receive payment on the invoice for the same amount and deposit it into the Clearing Account.  That will zero out the Clearing Account leaving the balance due on the invoice.

If you're applying A/R to A/P, receive payment on the invoice and deposit it into the Clearing Account.  Then, pay the bill for the same amount using the Clearing Account.  That will zero out the Clearing Account leaving the balance due on the bill.