How do I move an unapplied (over) payment in QBO to the outstanding balance of a later invoice and also show the credit paid against the later bill?

$50,000 was moved to a bank account.  At the time, $43,305.62 in invoices and bills were paid.  This left an unapplied credit of $6,694.38 showing on the invoice side.  The next two invoices and bills were paid $6,694.38 less, because of the overpayment.  What do I need to do in QBO to 1) apply the unapplied payment to the invoice?  2) apply the $6,694.38 to the outstanding amount left to pay on the bill? so that everything is properly applied and cleared in QBO.  The actual second reduced payment was "matched" in both bank accounts to the amount actually paid which was $6,694.38 less.  This was a transaction between two company accounts.